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- EMDB-10480: Structure of complete, activated transcription complex Pol II-DSI... -

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Basic information

Entry
Database: EMDB / ID: EMD-10480
TitleStructure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1 (Map 1)
Map dataB factor of -115 applied
Sample
  • Complex: Complete EC*
    • Complex: Pig DNA/RNA polymerase subunits
      • Protein or peptide: x 12 types
    • Complex: Human transcription factors and associated proteins
      • Protein or peptide: x 7 types
    • Complex: DNA/RNA
      • DNA: x 2 types
      • RNA: x 1 types
    • Complex: Transcription elongation factor SPT4 and SPT5
      • Protein or peptide: x 2 types
  • Ligand: x 2 types
Function / homology
Function and homology information


blastocyst growth / inner cell mass cell differentiation / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / negative regulation of DNA-templated transcription, elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / regulation of isotype switching ...blastocyst growth / inner cell mass cell differentiation / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / negative regulation of DNA-templated transcription, elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / blastocyst hatching / positive regulation of cell cycle G1/S phase transition / DSIF complex / regulation of transcription elongation by RNA polymerase II / nucleosome organization / trophectodermal cell differentiation / regulation of mRNA processing / mRNA 3'-end processing / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / blastocyst formation / : / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription elongation-coupled chromatin remodeling / negative regulation of gene expression, epigenetic / negative regulation of G1/S transition of mitotic cell cycle / stem cell population maintenance / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / interleukin-6-mediated signaling pathway / mRNA Capping / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / tRNA transcription by RNA polymerase III / organelle membrane / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cell surface receptor signaling pathway via JAK-STAT / positive regulation of translational initiation / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / protein localization to nucleus / positive regulation of Wnt signaling pathway / transcription-coupled nucleotide-excision repair / nucleosome binding / Tat-mediated elongation of the HIV-1 transcript / RNA polymerase II activity / mRNA transport / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / rescue of stalled ribosome / translation initiation factor binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / RNA Polymerase II Pre-transcription Events / SH2 domain binding
Similarity search - Function
Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / HHH domain 9 / HHH domain / Leo1-like protein / Leo1-like protein / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. ...Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / HHH domain 9 / HHH domain / Leo1-like protein / Leo1-like protein / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal / RNA polymerase II associated factor Paf1 / Paf1 / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / Spt5, KOW domain repeat 6 / YqgF/RNase H-like domain superfamily / Tetratricopeptide repeat / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / Tetratricopeptide repeat / RNA-binding domain, S1 / RuvA domain 2-like / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Tetratricopeptide repeat / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal
Similarity search - Domain/homology
RNA polymerase II subunit D / Uncharacterized protein / : / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 ...RNA polymerase II subunit D / Uncharacterized protein / : / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription elongation factor SPT4 / Parafibromin / RNA polymerase-associated protein CTR9 homolog / Transcription elongation factor SPT6 / RNA polymerase II-associated factor 1 homolog / RNA polymerase-associated protein LEO1 / RNA polymerase-associated protein RTF1 homolog / Superkiller complex protein 8
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human) / synthetic construct (others) / Pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVos SM / Farnung L / Cramer P
Funding support Germany, 4 items
OrganizationGrant numberCountry
European Research Council693023 Germany
German Research FoundationSFB860 Germany
German Research FoundationSFB860 Germany
Volkswagen Foundation Germany
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation.
Authors: Seychelle M Vos / Lucas Farnung / Andreas Linden / Henning Urlaub / Patrick Cramer /
Abstract: Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation ...Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation factors DSIF, PAF1 complex (PAF) and SPT6. Here we report the cryo-EM structure of the complete EC* that contains RTF1, a dissociable PAF subunit critical for chromatin transcription. The RTF1 Plus3 domain associates with Pol II subunit RPB12 and the phosphorylated C-terminal region of DSIF subunit SPT5. RTF1 also forms four α-helices that extend from the Plus3 domain along the Pol II protrusion and RPB10 to the polymerase funnel. The C-terminal 'fastener' helix retains PAF and is followed by a 'latch' that reaches the end of the bridge helix, a flexible element of the Pol II active site. RTF1 strongly stimulates Pol II elongation, and this requires the latch, possibly suggesting that RTF1 activates transcription allosterically by influencing Pol II translocation.
History
DepositionNov 11, 2019-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ted
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ted
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ted
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10480.png

Downloads & links

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Map

FileDownload / File: emd_10480.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB factor of -115 applied
Voxel sizeX=Y=Z: 1.049 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.085893884 - 0.16493231
Average (Standard dev.)0.00033805167 (±0.0043800185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 377.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0491.0491.049
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z377.640377.640377.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0860.1650.000

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Supplemental data

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Mask #1

Fileemd_10480_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram (log scale)

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Mask #2

Fileemd_10480_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Composite map used for model refinement. Generated using maps 1, 2,

Fileemd_10480_additional.map
AnnotationComposite map used for model refinement. Generated using maps 1, 2,
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10480_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10480_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complete EC*

EntireName: Complete EC*
Components
  • Complex: Complete EC*
    • Complex: Pig DNA/RNA polymerase subunits
      • Protein or peptide: DNA-directed RNA polymerase subunitPolymerase
      • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
      • Protein or peptide: RNA polymerase II subunit C
      • Protein or peptide: RNA polymerase II subunit D
      • Protein or peptide: RNA polymerase II subunit E
      • Protein or peptide: RNA polymerase II subunit F
      • Protein or peptide: RNA polymerase II subunit G
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9Polymerase
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Uncharacterized protein
      • Protein or peptide: Uncharacterized protein
    • Complex: Human transcription factors and associated proteins
      • Protein or peptide: Transcription elongation factor SPT6
      • Protein or peptide: RNA polymerase-associated protein CTR9 homolog
      • Protein or peptide: RNA polymerase-associated protein RTF1 homolog
      • Protein or peptide: RNA polymerase-associated protein LEO1
      • Protein or peptide: RNA polymerase II-associated factor 1 homolog
      • Protein or peptide: WD repeat-containing protein 61
      • Protein or peptide: Parafibromin
    • Complex: DNA/RNA
      • DNA: DNA (37-MER)
      • RNA: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')
      • DNA: Template DNA
    • Complex: Transcription elongation factor SPT4 and SPT5
      • Protein or peptide: Transcription elongation factor SPT4
      • Protein or peptide: Transcription elongation factor SPT5
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complete EC*

SupramoleculeName: Complete EC* / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24
Molecular weightTheoretical: 1.34 MDa

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Supramolecule #2: Pig DNA/RNA polymerase subunits

SupramoleculeName: Pig DNA/RNA polymerase subunits / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: Human transcription factors and associated proteins

SupramoleculeName: Human transcription factors and associated proteins / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13, #16-#17, #19-#22
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #4: DNA/RNA

SupramoleculeName: DNA/RNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #14-#15, #18
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Supramolecule #5: Transcription elongation factor SPT4 and SPT5

SupramoleculeName: Transcription elongation factor SPT4 and SPT5 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #23-#24
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 219.0495 KDa
SequenceString: MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE M DNKFGVEQ ...String:
MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE M DNKFGVEQ PEGDEDLTKE KGHGGCGRYQ PRIRRSGLEL YAEWKHVNED SQEKKILLSP ERVHEIFKRI SDEECFVLGM EP RYARPEW MIVTVLPVPP LSVRPAVVMQ GSARNQDDLT HKLADIVKIN NQLRRNEQNG AAAHVIAEDV KLLQFHVATM VDN ELPGLP RAMQKSGRPL KSLKQRLKGK EGRVRGNLMG KRVDFSARTV ITPDPNLSID QVGVPRSIAA NMTFAEIVTP FNID RLQEL VRRGNSQYPG AKYIIRDNGD RIDLRFHPKP SDLHLQTGYK VERHMCDGDI VIFNRQPTLH KMSMMGHRVR ILPWS TFRL NLSVTTPYNA DFDGDEMNLH LPQSLETRAE IQELAMVPRM IVTPQSNRPV MGIVQDTLTA VRKFTKRDVF LERGEV MNL LMFLSTWDGK VPQPAILKPR PLWTGKQIFS LIIPGHINCI RTHSTHPDDE DSGPYKHISP GDTKVVVENG ELIMGIL CK KSLGTSAGSL VHISYLEMGH DITRLFYSNI QTVINNWLLI EGHTIGIGDS IADSKTYQDI QNTIKKAKQD VIEVIEKA H NNELEPTPGN TLRQTFENQV NRILNDARDK TGSSAQKSLS EYNNFKSMVV SGAKGSKINI SQVIAVVGQQ NVEGKRIPF GFKHRTLPHF IKDDYGPESR GFVENSYLAG LTPTEFFFHA MGGREGLIDT AVKTAETGYI QRRLIKSMES VMVKYDATVR NSINQVVQL RYGEDGLAGE SVEFQNLATL KPSNKAFEKK FRFDYTNERA LRRTLQEDLV KDVLSNAHIQ NELEREFERM R EDREVLRV IFPTGDSKVV LPCNLLRMIW NAQKIFHINP RLPSDLHPIK VVEGVKELSK KLVIVNGDDP LSRQAQENAT LL FNIHLRS TLCSRRMAEE FRLSGEAFDW LLGEIESKFN QAIAHPGEMV GALAAQSLGE PATQMTLNTF HYAGVSAKNV TLG VPRLKE LINISKKPKT PSLTVFLLGQ SARDAERAKD ILCRLEHTTL RKVTANTAIY YDPNPQSTVV AEDQEWVNVY YEMP DFDVA RISPWLLRVE LDRKHMTDRK LTMEQIAEKI NAGFGDDLNC IFNDDNAEKL VLRIRIMNSD ENKMQEEEEV VDKMD DDVF LRCIESNMLT DMTLQGIEQI SKVYMHLPQT DNKKKIIITE DGEFKALQEW ILETDGVSLM RVLSEKDVDP VRTTSN DIV EIFTVLGIEA VRKALERELY HVISFDGSYV NYRHLALLCD TMTCRGHLMA ITRHGVNRQD TGPLMKCSFE ETVDVLM EA AAHGESDPMK GVSENIMLGQ LAPAGTGCFD LLLDAEKCKY GMEIPTNIPG LGAAGPTGMF FGSAPSPMGG ISPAMTPW N QGA(TPO)PAYGAW SPSVGSGMTP GAAGF(SEP)PSAA SDASGFSPGY SPAWSPTPGS PGSPGPSSPY IPSPGGAMSP S YSPTSPAY EPRSPGGYTP QSPSYSPTSP SYSPTSPSYS PTSPNYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YS PTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTS PSYSPT SPNYSPTSPN YTPTSPSYSP TSPSYSPTSP NYTPTSPNYS PTSPSYSPTS PSYSPTSPSY SPSSPRYTPQ SPTY TPSSP SYSPSSPSYS PTSPKYTPTS PSYSPSSPEY TPTSPKYSPT SPKYSPTSPK YSPTSPTYSP TTPKYSPTSP TYSPT SPVY TPTSPKYSPT SPTYSPTSPK YSPTSPTYSP TSPKGSTYSP TSPGYSPTSP TYSLTSPAIS PDDSDEEN

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Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 142.426125 KDa
SequenceString: MCSTNLSQAL AYFRAGANLT AASLWAGFRG SRRIFWERRK RKSLCLALRP GGACWRWLLA VSCVSLRGLG APGSCANMYD ADEDMQYDE DDDEITPDLW QEACWIVISS YFDEKGLVRQ QLDSFDEFIQ MSVQRIVEDA PPIDLQAEAQ HASGEVEEPP R YLLKFEQI ...String:
MCSTNLSQAL AYFRAGANLT AASLWAGFRG SRRIFWERRK RKSLCLALRP GGACWRWLLA VSCVSLRGLG APGSCANMYD ADEDMQYDE DDDEITPDLW QEACWIVISS YFDEKGLVRQ QLDSFDEFIQ MSVQRIVEDA PPIDLQAEAQ HASGEVEEPP R YLLKFEQI YLSKPTHWER DGAPSPMMPN EARLRNLTYS APLYVDITKT VIKEGEEQLQ TQHQKTFIGK IPIMLRSTYC LL NGLTDRD LCELNECPLD PGGYFIINGS EKVLIAQEKM ATNTVYVFAK KDSKYAYTGE CRSCLENSSR PTSTIWVSML ARG GQGAKK SAIGQRIVAT LPYIKQEVPI IIVFRALGFV SDRDILEHII YDFEDPEMME MVKPSLDEAF VIQEQNVALN FIGS RGAKP GVTKEKRIKY AKEVLQKEML PHVGVSDFCE TKKAYFLGYM VHRLLLAALG RRELDDRDHY GNKRLDLAGP LLAFL FRGM FKNLLKEVRI YAQKFIDRGK DFNLELAIKT RIISDGLKYS LATGNWGDQK KAHQARAGVS QVLNRLTFAS TLSHLR RLN SPIGRDGKLA KPRQLHNTLW GMVCPAETPE GHAVGLVKNL ALMAYISVGS QPSPILEFLE EWSMENLEEI SPAAIAD AT KIFVNGCWVG IHKDPEQLMN TLRKLRRQMD IIVSEVSMIR DIREREIRIY TDAGRICRPL LIVEKQKLLL KKRHIDQL K EREYNNYSWQ DLVASGVVEY IDTLEEETVM LAMTPDDLQE KEVAYCSTYT HCEIHPSMIL GVCASIIPFP DHNQSPRNT YQSAMGKQAM GVYITNFHVR MDTLAHVLYY PQKPLVTTRS MEYLRFRELP AGINSIVAIA SYTGYNQEDS VIMNRSAVDR GFFRSVFYR SYKEQESKKG FDQEEVFEKP TRETCQGMRH AIYDKLDDDG LIAPGVRVSG DDVIIGKTVT LPENEDELEG T NRRYTKRD CSTFLRTSET GIVDQVMVTL NQEGYKFCKI RVRSVRIPQI GDKFASRHGQ KGTCGIQYRQ EDMPFTCEGI TP DIIINPH AIPSRMTIGH LIECLQGKVS ANKGEIGDAT PFNDAVNVQK ISNLLSDYGY HLRGNEVLYN GFTGRKITSQ IFI GPTYYQ RLKHMVDDKI HSRARGPIQI LNRQPMEGRS RDGGLRFGEM ERDCQIAHGA AQFLRERLFE ASDPYQVHVC NLCG IMAIA NTRTHTYECR GCRNKTQISL VRMPYACKLL FQELMSMSIA PRMMSV

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Macromolecule #3: RNA polymerase II subunit C

MacromoleculeName: RNA polymerase II subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 31.439074 KDa
SequenceString: MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP SDYVEQDDIL IVKLRKGQEL R LRAYAKKG ...String:
MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP SDYVEQDDIL IVKLRKGQEL R LRAYAKKG FGKEHAKWNP TAGVAFEYDP DNALRHTVYP KPEEWPKSEY SELDEDESQA PYDPNGKPER FYYNVESCGS LR PETIVLS ALSGLKKKLS DLQTQLSHEI QSDVLTIN

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Macromolecule #4: RNA polymerase II subunit D

MacromoleculeName: RNA polymerase II subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 16.331255 KDa
SequenceString:
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQ KKLHKFELAC LANLCPETAE ESKALIPSLE GRFEDEELQQ ILDDIQTKRS FQY

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Macromolecule #5: RNA polymerase II subunit E

MacromoleculeName: RNA polymerase II subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 24.644318 KDa
SequenceString: MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN ...String:
MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN QLPRIQAGDP VARYFGIKRG QVVKIIRPSE TAGRYITYRL VQ

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Macromolecule #6: RNA polymerase II subunit F

MacromoleculeName: RNA polymerase II subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 14.477001 KDa
SequenceString:
MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIISD

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Macromolecule #7: RNA polymerase II subunit G

MacromoleculeName: RNA polymerase II subunit G / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 19.314283 KDa
SequenceString:
MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYPV KYKAIVFRPF KGEVVDAVV TQVNKVGLFT EIGPMSCFIS RHSIPSEMEF DPNSNPPCYK TMDEDIVIQQ DDEIRLKIVG TRVDKNDIFA I GSLMDDYL GLVS

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Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 17.162273 KDa
SequenceString:
MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGTL DDGEYNPTDD RPSRADQFE YVMYGKVYRI EGDETSTEAA TRLSAYVSYG GLLMRLQGDA NNLHGFEVDS RVYLLMKKLA F

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Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 14.541221 KDa
SequenceString:
MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQIIA DVSQDPTLPR TEDHPCQKC GHKEAVFFQS HSARAEDAMR LYYVCTAPHC GHRWTE

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Macromolecule #10: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 7.655123 KDa
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

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Macromolecule #11: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 13.310284 KDa
SequenceString:
MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEHK IIIRVQTTPD YSPQEAFTN AITDLISELS LLEERFRVAI KDKQEGIE

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Macromolecule #12: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 7.018244 KDa
SequenceString:
MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

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Macromolecule #13: Transcription elongation factor SPT6

MacromoleculeName: Transcription elongation factor SPT6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 199.602969 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMSDFVES EAEESEEEYN DEGEVVPRVT KKFVEEEDDD EEEEEENLDD QDEQGNLKGF INDDDDEDEG EEDEGSDSGD SEDDVGHKK RKRTSFDDRL EDDDFDLIEE NLGVKVKRGQ KYRRVKKMSD DEDDDEEEYG KEEHEKEAIA EEIFQDGEGE E GQEAMEAP ...String:
SNAMSDFVES EAEESEEEYN DEGEVVPRVT KKFVEEEDDD EEEEEENLDD QDEQGNLKGF INDDDDEDEG EEDEGSDSGD SEDDVGHKK RKRTSFDDRL EDDDFDLIEE NLGVKVKRGQ KYRRVKKMSD DEDDDEEEYG KEEHEKEAIA EEIFQDGEGE E GQEAMEAP MAPPEEEEED DEESDIDDFI VDDDGQPLKK PKWRKKLPGY TDAALQEAQE IFGVDFDYDE FEKYNEYDEE LE EEYEYED DEAEGEIRVR PKKTTKKRVS RRSIFEMYEP SELESSHLTD QDNEIRATDL PERFQLRSIP VKGAEDDELE EEA DWIYRN AFATPTISLQ ESCDYLDRGQ PASSFSRKGP STIQKIKEAL GFMRNQHFEV PFIAFYRKEY VEPELHINDL WRVW QWDEK WTQLRIRKEN LTRLFEKMQA YQYEQISADP DKPLADGIRA LDTTDMERLK DVQSMDELKD VYNHFLLYYG RDIPK MQNA AKASRKKLKR VREEGDEEGE GDEAEDEEQR GPELKQASRR DMYTICQSAG LDGLAKKFGL TPEQFGENLR DSYQRH ETE QFPAEPLELA KDYVCSQFPT PEAVLEGARY MVALQIAREP LVRQVLRQTF QERAKLNITP TKKGRKDVDE AHYAYSF KY LKNKPVKELR DDQFLKICLA EDEGLLTTDI SIDLKGVEGY GNDQTYFEEI KQFYYRDEFS HQVQEWNRQR TMAIERAL Q QFLYVQMAKE LKNKLLAEAK EYVIKACSRK LYNWLRVAPY RPDQQVEEDD DFMDENQGKG IRVLGIAFSS ARDHPVFCA LVNGEGEVTD FLRLPHFTKR RTAWREEERE KKAQDIETLK KFLLNKKPHV VTVAGENRDA QMLIEDVKRI VHELDQGQQL SSIGVELVD NELAILYMNS KKSEAEFRDY PPVLRQAVSL ARRIQDPLIE FAQVCSSDED ILCLKFHPLQ EHVVKEELLN A LYCEFINR VNEVGVDVNR AIAHPYSQAL IQYVCGLGPR KGTHLLKILK QNNTRLESRT QLVTMCHMGP KVFMNCAGFL KI DTASLGD STDSYIEVLD GSRVHPETYE WARKMAVDAL EYDESAEDAN PAGALEEILE NPERLKDLDL DAFAEELERQ GYG DKHITL YDIRAELSCR YKDLRTAYRS PNTEEIFNML TKETPETFYI GKLIICNVTG IAHRRPQGES YDQAIRNDET GLWQ CPFCQ QDNFPELSEV WNHFDSGSCP GQAIGVKTRL DNGVTGFIPT KFLSDKVVKR PEERVKVGMT VHCRIMKIDI EKFSA DLTC RTSDLMDRNN EWKLPKDTYY DFDAEAADHK QEEDMKRKQQ RTTYIKRVIA HPSFHNINFK QAEKMMETMD QGDVII RPS SKGENHLTVT WKVSDGIYQH VDVREEGKEN AFSLGATLWI NSEEFEDLDE IVARYVQPMA SFARDLLNHK YYQDCSG GD RKKLEELLIK TKKEKPTFIP YFICACKELP GKFLLGYQPR GKPRIEYVTV TPEGFRYRGQ IFPTVNGLFR WFKDHYQD P VPGITPSSSS RTRTPASINA TPANINLADL TRAVNALPQN MTSQMFSAIA AVTGQGQNPN ATPAQWASSQ YGYGGSGGG SSAYHVFPTP AQQPVATPLM TPSYSYTTPS QPITTPQYHQ LQASTTPQSA QAQPQPSSSS RQRQQQPKSN SHAAIDWGKM AEQWLQEKE AERRKQKQRL TPRPSPSPMI ESTPMSIAGD ATPLLDEMDR

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Macromolecule #16: RNA polymerase-associated protein CTR9 homolog

MacromoleculeName: RNA polymerase-associated protein CTR9 homolog / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 134.510203 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSRGSIEIPL RDTDEVIELD FDQLPEGDEV ISILKQEHTQ LHIWIALALE YYKQGKTEEF VKLLEAARID GNLDYRDHEK DQMTCLDTL AAYYVQQARK EKNKDNKKDL ITQATLLYTM ADKIIMYDQN HLLGRACFCL LEGDKMDQAD AQFHFVLNQS P NNIPALLG ...String:
MSRGSIEIPL RDTDEVIELD FDQLPEGDEV ISILKQEHTQ LHIWIALALE YYKQGKTEEF VKLLEAARID GNLDYRDHEK DQMTCLDTL AAYYVQQARK EKNKDNKKDL ITQATLLYTM ADKIIMYDQN HLLGRACFCL LEGDKMDQAD AQFHFVLNQS P NNIPALLG KACISFNKKD YRGALAYYKK ALRTNPGCPA EVRLGMGHCF VKLNKLEKAR LAFSRALELN SKCVGALVGL AV LELNNKE ADSIKNGVQL LSRAYTIDPS NPMVLNHLAN HFFFKKDYSK VQHLALHAFH NTEVEAMQAE SCYQLARSFH VQE DYDQAF QYYYQATQFA SSSFVLPFFG LGQMYIYRGD KENASQCFEK VLKAYPNNYE TMKILGSLYA ASEDQEKRDI AKGH LKKVT EQYPDDVEAW IELAQILEQT DIQGALSAYG TATRILQEKV QADVPPEILN NVGALHFRLG NLGEAKKYFL ASLDR AKAE AEHDEHYYNA ISVTTSYNLA RLYEAMCEFH EAEKLYKNIL REHPNYVDCY LRLGAMARDK GNFYEASDWF KEALQI NQD HPDAWSLIGN LHLAKQEWGP GQKKFERILK QPSTQSDTYS MLALGNVWLQ TLHQPTRDRE KEKRHQDRAL AIYKQVL RN DAKNLYAANG IGAVLAHKGY FREARDVFAQ VREATADISD VWLNLAHIYV EQKQYISAVQ MYENCLRKFY KHQNTEVV L YLARALFKCG KLQECKQTLL KARHVAPSDT VLMFNVALVL QRLATSVLKD EKSNLKEVLN AVKELELAHR YFSYLSKVG DKMRFDLALA ATEARQCSDL LSQAQYHVAR ARKQDEEERE LRAKQEQEKE LLRQKLLKEQ EEKRLREKEE QKKLLEQRAQ YVEKTKNIL MFTGETEATK EKKRGGGGGR RSKKGGEFDE FVNDDTDDDL PISKKKKRRK GSGSEQEGED EEGGERKKKK R RRHPKGEE GSDDDETENG PKPKKRRPPK AEKKKAPKPE RLPPSMKGKI KSKAIISSSD DSSDEDKLKI ADEGHPRNSN SN SDSDEDE QRKKCASSES DSDENQNKSG SEAGSPRRPR RQRSDQDSDS DQPSRKRRPS GSEQSDNESV QSGRSHSGVS END SRPASP SAESDHESER GSDNEGSGQG SGNESEPEGS NNEASDRGSE HGSDDSDENL YFQ

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Macromolecule #17: RNA polymerase-associated protein RTF1 homolog

MacromoleculeName: RNA polymerase-associated protein RTF1 homolog / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.733016 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMRGRLCV GRAAAAAAAV AVPLAGGQEG SPGGGRRGSR GTTMVKKRKG RVVIDSDTED SGSDENLDQE LLSLAKRKRS DSEEKEPPV SQPAASSDSE TSDSDDEWTF GSNKNKKKGK ARKIEKKGTM KKQANKTASS GSSDKDSSAE SSAPEEGEVS D SDSNSSSS ...String:
SNAMRGRLCV GRAAAAAAAV AVPLAGGQEG SPGGGRRGSR GTTMVKKRKG RVVIDSDTED SGSDENLDQE LLSLAKRKRS DSEEKEPPV SQPAASSDSE TSDSDDEWTF GSNKNKKKGK ARKIEKKGTM KKQANKTASS GSSDKDSSAE SSAPEEGEVS D SDSNSSSS SSDSDSSSED EEFHDGYGED LMGDEEDRAR LEQMTEKERE QELFNRIEKR EVLKRRFEIK KKLKTAKKKE KK EKKKKQE EEQEKKKLTQ IQESQVTSHN KERRSKRDEK LDKKSQAMEE LKAEREKRKN RTAELLAKKQ PLKTSEVYSD DEE EEEDDK SSEKSDRSSR TSSSDEEEEK EEIPPKSQPV SLPEELNRVR LSRHKLERWC HMPFFAKTVT GCFVRIGIGN HNSK PVYRV AEITGVVETA KVYQLGGTRT NKGLQLRHGN DQRVFRLEFV SNQEFTESEF MKWKEAMFSA GMQLPTLDEI NKKEL SIKE ALNYKFNDQD IEEIVKEKER FRKAPPNYAM KKTQLLKEKA MAEDLGDQDK AKQIQDQLNE LEERAEALDR QRTKNI SAI SYINQRNREW NIVESEKALV AESHNMKNQQ MDPFTRRQCK PTIVSNSRDP AVQAAILAQL NAKYGSGVLP DAPKEMS KG QGKDKDLNSK SASDLSEDLF KVHDFDVKID LQVPSSESKA LAITSKAPPA KDGAPRRSLN LEDYKKRRGL I

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Macromolecule #19: RNA polymerase-associated protein LEO1

MacromoleculeName: RNA polymerase-associated protein LEO1 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.514172 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADMEDLFGS DADSEAERKD SDSGSDSDSD QENAASGSNA SGSESDQDER GDSGQPSNKE LFGDDSEDEG ASHHSGSDNH SERSDNRSE ASERSDHEDN DPSDVDQHSG SEAPNDDEDE GHRSDGGSHH SEAEGSEKAH SDDEKWGRED KSDQSDDEKI Q NSDDEERA ...String:
MADMEDLFGS DADSEAERKD SDSGSDSDSD QENAASGSNA SGSESDQDER GDSGQPSNKE LFGDDSEDEG ASHHSGSDNH SERSDNRSE ASERSDHEDN DPSDVDQHSG SEAPNDDEDE GHRSDGGSHH SEAEGSEKAH SDDEKWGRED KSDQSDDEKI Q NSDDEERA QGSDEDKLQN SDDDEKMQNT DDEERPQLSD DERQQLSEEE KANSDDERPV ASDNDDEKQN SDDEEQPQLS DE EKMQNSD DERPQASDEE HRHSDDEEEQ DHKSESARGS DSEDEVLRMK RKNAIASDSE ADSDTEVPKD NSGTMDLFGG ADD ISSGSD GEDKPPTPGQ PVDENGLPQD QQEEEPIPET RIEVEIPKVN TDLGNDLYFV KLPNFLSVEP RPFDPQYYED EFED EEMLD EEGRTRLKLK VENTIRWRIR RDEEGNEIKE SNARIVKWSD GSMSLHLGNE VFDVYKAPLQ GDHNHLFIRQ GTGLQ GQAV FKTKLTFRPH STDSATHRKM TLSLADRCSK TQKIRILPMA GRDPECQRTE MIKKEEERLR ASIRRESQQR RMREKQ HQR GLSASYLEPD RYDEEEEGEE SISLAAIKNR YKGGIREERA RIYSSDSDEG SEEDKAQRLL KAKKLTSDEE GEPSGKR KA EDDDKANKKH KKYVISDEEE EDDD

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Macromolecule #20: RNA polymerase II-associated factor 1 homolog

MacromoleculeName: RNA polymerase II-associated factor 1 homolog / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.052672 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAPTIQTQAQ REDGHRPNSH RTLPERSGVV CRVKYCNSLP DIPFDPKFIT YPFDQNRFVQ YKATSLEKQH KHDLLTEPDL GVTIDLINP DTYRIDPNVL LDPADEKLLE EEIQAPTSSK RSQQHAKVVP WMRKTEYIST EFNRYGISNE KPEVKIGVSV K QQFTEEEI ...String:
MAPTIQTQAQ REDGHRPNSH RTLPERSGVV CRVKYCNSLP DIPFDPKFIT YPFDQNRFVQ YKATSLEKQH KHDLLTEPDL GVTIDLINP DTYRIDPNVL LDPADEKLLE EEIQAPTSSK RSQQHAKVVP WMRKTEYIST EFNRYGISNE KPEVKIGVSV K QQFTEEEI YKDRDSQITA IEKTFEDAQK SISQHYSKPR VTPVEVMPVF PDFKMWINPC AQVIFDSDPA PKDTSGAAAL EM MSQAMIR GMMDEEGNQF VAYFLPVEET LKKRKRDQEE EMDYAPDDVY DYKIAREYNW NVKNKASKGY EENYFFIFRE GDG VYYNEL ETRVRLSKRR AKAGVQSGTN ALLVVKHRDM NEKELEAQEA RKAQLENHEP EEEEEEEMET EEKEAGGSDE EQEK GSSSE KEGSEDEHSG SESEREEGDR DEASDKSGSG EDESSEDEAR AARDKEEIFG SDADSEDDAD SDDEDRGQAQ GGSDN DSDS GSNGGGQRSR SHSRSASPFP SGSEHSAQED GSEAAASDSS EADSDSD

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Macromolecule #21: WD repeat-containing protein 61

MacromoleculeName: WD repeat-containing protein 61 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.617465 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTNQYGILFK QEQAHDDAIW SVAWGTNKKE NSETVVTGSL DDLVKVWKWR DERLDLQWSL EGHQLGVVSV DISHTLPIAA SSSLDAHIR LWDLENGKQI KSIDAGPVDA WTLAFSPDSQ YLATGTHVGK VNIFGVESGK KEYSLDTRGK FILSIAYSPD G KYLASGAI ...String:
MTNQYGILFK QEQAHDDAIW SVAWGTNKKE NSETVVTGSL DDLVKVWKWR DERLDLQWSL EGHQLGVVSV DISHTLPIAA SSSLDAHIR LWDLENGKQI KSIDAGPVDA WTLAFSPDSQ YLATGTHVGK VNIFGVESGK KEYSLDTRGK FILSIAYSPD G KYLASGAI DGIINIFDIA TGKLLHTLEG HAMPIRSLTF SPDSQLLVTA SDDGYIKIYD VQHANLAGTL SGHASWVLNV AF CPDDTHF VSSSSDKSVK VWDVGTRTCV HTFFDHQDQV WGVKYNGNGS KIVSVGDDQE IHIYDCPI

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Macromolecule #22: Parafibromin

MacromoleculeName: Parafibromin / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.673539 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADVLSVLRQ YNIQKKEIVV KGDEVIFGEF SWPKNVKTNY VVWGTGKEGQ PREYYTLDSI LFLLNNVHLS HPVYVRRAAT ENIPVVRRP DRKDLLGYLN GEASTSASID RSAPLEIGLQ RSTQVKRAAD EVLAEAKKPR IEDEECVRLD KERLAARLEG H KEGIVQTE ...String:
MADVLSVLRQ YNIQKKEIVV KGDEVIFGEF SWPKNVKTNY VVWGTGKEGQ PREYYTLDSI LFLLNNVHLS HPVYVRRAAT ENIPVVRRP DRKDLLGYLN GEASTSASID RSAPLEIGLQ RSTQVKRAAD EVLAEAKKPR IEDEECVRLD KERLAARLEG H KEGIVQTE QIRSLSEAMS VEKIAAIKAK IMAKKRSTIK TDLDDDITAL KQRSFVDAEV DVTRDIVSRE RVWRTRTTIL QS TGKNFSK NIFAILQSVK AREEGRAPEQ RPAPNAAPVD PTLRTKQPIP AAYNRYDQER FKGKEETEGF KIDTMGTYHG MTL KSVTEG ASARKTQTPA AQPVPRPVSQ ARPPPNQKKG SRTPIIIIPA ATTSLITMLN AKDLLQDLKF VPSDEKKKQG CQRE NETLI QRRKDQMQPG GTAISVTVPY RVVDQPLKLM PQDWDRVVAV FVQGPAWQFK GWPWLLPDGS PVDIFAKIKA FHLKY DEVR LDPNVQKWDV TVLELSYHKR HLDRPVFLRF WETLDRYMVK HKSHLRF

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Macromolecule #23: Transcription elongation factor SPT4

MacromoleculeName: Transcription elongation factor SPT4 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.508496 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGSMALETV PKDLRHLRAC LLCSLVKTID QFEYDGCDNC DAYLQMKGNR EMVYDCTSSS FDGIIAMMSP EDSWVSKWQR VSNFKPGVY AVSVTGRLPQ GIVRELKSRG VAYKSRDTAI KT

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Macromolecule #24: Transcription elongation factor SPT5

MacromoleculeName: Transcription elongation factor SPT5 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 121.225477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDSEDSNFS EEEDSERSSD GEEAEVDEER RSAAGSEKEE EPEDEEEEEE EEEYDEEEEE EDDDRPPKKP RHGGFILDEA DVDDEYEDE DQWEDGAEDI LEKEEIEASN IDNVVLDEDR SGARRLQNLW RDQREEELGE YYMKKYAKSS VGETVYGGSD E LSDDITQQ ...String:
MSDSEDSNFS EEEDSERSSD GEEAEVDEER RSAAGSEKEE EPEDEEEEEE EEEYDEEEEE EDDDRPPKKP RHGGFILDEA DVDDEYEDE DQWEDGAEDI LEKEEIEASN IDNVVLDEDR SGARRLQNLW RDQREEELGE YYMKKYAKSS VGETVYGGSD E LSDDITQQ QLLPGVKDPN LWTVKCKIGE ERATAISLMR KFIAYQFTDT PLQIKSVVAP EHVKGYIYVE AYKQTHVKQA IE GVGNLRL GYWNQQMVPI KEMTDVLKVV KEVANLKPKS WVRLKRGIYK DDIAQVDYVE PSQNTISLKM IPRIDYDRIK ARM SLKDWF AKRKKFKRPP QRLFDAEKIR SLGGDVASDG DFLIFEGNRY SRKGFLFKSF AMSAVITEGV KPTLSELEKF EDQP EGIDL EVVTESTGKE REHNFQPGDN VEVCEGELIN LQGKILSVDG NKITIMPKHE DLKDMLEFPA QELRKYFKMG DHVKV IAGR FEGDTGLIVR VEENFVILFS DLTMHELKVL PRDLQLCSET ASGVDVGGQH EWGELVQLDP QTVGVIVRLE RETFQV LNM YGKVVTVRHQ AVTRKKDNRF AVALDSEQNN IHVKDIVKVI DGPHSGREGE IRHLFRSFAF LHCKKLVENG GMFVCKT RH LVLAGGSKPR DVTNFTVGGF APMSPRISSP MHPSAGGQRG GFGSPGGGSG GMSRGRGRRD NELIGQTVRI SQGPYKGY I GVVKDATEST ARVELHSTCQ TISVDRQRLT TVGSRRPGGM TSTYGRTPMY GSQ(TPO)PMYGSG SRTPMYGSQT PLQDG SRTP HYGSQTPLHD GSRTPAQSGA WDPNNPNTPS RAEEEYEYAF DDEPTPSPQA YGGTPNPQTP GYPDPSSPQV NPQYNP QTP GTPAMYNTDQ FSPYAAPSPQ GSYQPSPSPQ SYHQVAPSPA GYQNTHSPAS YHPTPSPMAY QASPSPSPVG YSPMTPG AP SPGGYNPHTP GSGIEQNSSD WVTTDIQVKV RDTYLDTQVV GQTGVIRSVT GGMCSVYLKD SEKVVSISSE HLEPITPT K NNKVKVILGE DREATGVLLS IDGEDGIVRM DLDEQLKILN LRFLGKLLEA

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Macromolecule #14: DNA (37-MER)

MacromoleculeName: DNA (37-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.932533 KDa
SequenceString:
(DC)(DC)(DA)(DT)(DT)(DG)(DA)(DG)(DA)(DG) (DC)(DG)(DG)(DC)(DC)(DC)(DT)(DT)(DG)(DT) (DG)(DT)(DT)(DC)(DA)(DG)(DG)(DA)(DG) (DC)(DC)(DA)(DG)(DC)(DA)(DG)(DG)(DG)(DA) (DG) (DC)(DT)(DG)(DG)(DG)(DA)(DG)(DC)

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Macromolecule #18: Template DNA

MacromoleculeName: Template DNA / type: dna / ID: 18 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.672335 KDa
SequenceString:
(DG)(DC)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DC)(DC)(DC)(DT)(DG)(DC)(DT)(DG)(DG)(DC) (DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG)(DG) (DG)(DT)(DT)(DC)(DT)(DG)(DC)(DC)(DG)(DC) (DT) (DC)(DT)(DC)(DA)(DA)(DT)(DG)(DG)

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Macromolecule #15: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP...

MacromoleculeName: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')
type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.843892 KDa
SequenceString:
UUAAGGAAUU AAGUCGUGCG UCUAAUAACC GGAGAGGGAA CCCACU

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Macromolecule #25: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 25 / Number of copies: 9 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #26: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 26 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
20.0 mMNa-HEPES
1.0 mMDTT
20.0 mMTRIS-HClTris
GridModel: UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 2 microliters applied to both sides of grid. Sample incubated on grid for 10s prior to blotting. Blotting for 8.5s..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 13679 / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 611983
CTF correctionSoftware - Name: Warp
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 446195
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model(PDB ID:

6gmh

,

4l1u

,

6afo

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 115
Output model

PDB-6ted:
Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1

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