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- EMDB-36162: Cryo-EM structure of yeast Rat1-bound Pol II pre-termination tran... -

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Basic information

Entry
Database: EMDB / ID: EMD-36162
TitleCryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 1 (Pol II Rat1-PTTC1)
Map data
Sample
  • Complex: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 and Spt5
    • Protein or peptide: x 15 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsTranscription termination / Pol II / Rat1/Rai1 / Spt5 / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase II termination complex / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / positive regulation of transcription elongation by RNA polymerase I / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / regulation of transcription-coupled nucleotide-excision repair / phosphodiesterase decapping endonuclease activity ...RNA polymerase II termination complex / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / positive regulation of transcription elongation by RNA polymerase I / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / regulation of transcription-coupled nucleotide-excision repair / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / termination of RNA polymerase II transcription, exosome-dependent / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / snRNP binding / 5'-3' RNA exonuclease activity / regulation of rRNA processing / intracellular mRNA localization / RNA polymerase I core binding / nucleic acid metabolic process / DSIF complex / nuclear mRNA surveillance / RNA polymerase I general transcription initiation factor binding / RPB4-RPB7 complex / U4 snRNA binding / : / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / RNA Polymerase I Transcription Initiation / transcription elongation-coupled chromatin remodeling / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / spliceosomal complex assembly / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase II complex binding / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / negative regulation of transcription elongation by RNA polymerase II / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / U5 snRNA binding / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / U2 snRNA binding / U6 snRNA binding / enzyme regulator activity / RNA polymerase II, core complex / positive regulation of autophagy / translation initiation factor binding / U1 snRNA binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / mRNA processing / rRNA processing / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / single-stranded DNA binding / ribosome biogenesis / chromosome
Similarity search - Function
5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain / RAI1-like / RAI1 like PD-(D/E)XK nuclease / RAI1-like family / Spt5 C-terminal nonapeptide repeat binding Spt4 ...5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain / RAI1-like / RAI1 like PD-(D/E)XK nuclease / RAI1-like family / Spt5 C-terminal nonapeptide repeat binding Spt4 / 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 / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / 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 / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit Rpo11 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB9 ...DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Decapping nuclease RAI1 / 5'-3' exoribonuclease 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZeng Y / Zhang Y
Funding support China, 2 items
OrganizationGrant numberCountry
Other governmentJCYJ-SHFY-2022-012 China
Other government2018YFA0900700 China
CitationJournal: Nature / Year: 2024
Title: Structural basis of exoribonuclease-mediated mRNA transcription termination.
Authors: Yuan Zeng / Hong-Wei Zhang / Xiao-Xian Wu / Yu Zhang /
Abstract: Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II ...Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II (Pol II). Here we report two cryogenic electron microscopy structures of Saccharomyces cerevisiae Pol II pre-termination transcription complexes bound to the 5'-to-3' exoribonuclease Rat1 and its partner Rai1. Our structures show that Rat1 displaces the elongation factor Spt5 to dock at the Pol II stalk domain. Rat1 shields the RNA exit channel of Pol II, guides the nascent RNA towards its active centre and stacks three nucleotides at the 5' terminus of the nascent RNA. The structures further show that Rat1 rotates towards Pol II as it shortens RNA. Our results provide the structural mechanism for the Rat1-mediated termination of mRNA transcription by Pol II in yeast and the exoribonuclease-mediated termination of mRNA transcription in other eukaryotes.
History
DepositionMay 11, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36162.png

Downloads & links

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Map

FileDownload / File: emd_36162.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.89535546 - 2.3521378
Average (Standard dev.)-0.0014003506 (±0.045312617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: local map

Fileemd_36162_additional_1.map
Annotationlocal map
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Additional map: composite map

Fileemd_36162_additional_2.map
Annotationcomposite map
Projections & Slices
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Half map: #1

Fileemd_36162_half_map_1.map
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Half map: #2

Fileemd_36162_half_map_2.map
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Sample components

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Entire : RNA Polymerase II pre-termination complex bound with Rat1-Rai1 an...

EntireName: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 and Spt5
Components
  • Complex: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 and Spt5
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1Polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB2Polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3Polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB4Polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB7Polymerase
    • 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: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11Polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
    • Protein or peptide: 5'-3' exoribonuclease 2
    • DNA: DNA (38-MER)
    • Protein or peptide: Decapping nuclease RAI1
    • RNA: RNA
    • DNA: DNA (38-MER)
    • Protein or peptide: Transcription elongation factor SPT5
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 an...

SupramoleculeName: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 and Spt5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 191.821578 KDa
SequenceString: MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG ...String:
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG NTQPTIRKDG LKLVGSWKKD RATGDADEPE LRVLSTEEIL NIFKHISVKD FTSLGFNEVF SRPEWMILTC LP VPPPPVR PSISFNESQR GEDDLTFKLA DILKANISLE TLEHNGAPHH AIEEAESLLQ FHVATYMDND IAGQPQALQK SGR PVKSIR ARLKGKEGRI RGNLMGKRVD FSARTVISGD PNLELDQVGV PKSIAKTLTY PEVVTPYNID RLTQLVRNGP NEHP GAKYV IRDSGDRIDL RYSKRAGDIQ LQYGWKVERH IMDNDPVLFN RQPSLHKMSM MAHRVKVIPY STFRLNLSVT SPYNA DFDG DEMNLHVPQS EETRAELSQL CAVPLQIVSP QSNKPCMGIV QDTLCGIRKL TLRDTFIELD QVLNMLYWVP DWDGVI PTP AIIKPKPLWS GKQILSVAIP NGIHLQRFDE GTTLLSPKDN GMLIIDGQII FGVVEKKTVG SSNGGLIHVV TREKGPQ VC AKLFGNIQKV VNFWLLHNGF STGIGDTIAD GPTMREITET IAEAKKKVLD VTKEAQANLL TAKHGMTLRE SFEDNVVR F LNEARDKAGR LAEVNLKDLN NVKQMVMAGS KGSFINIAQM SACVGQQSVE GKRIAFGFVD RTLPHFSKDD YSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGS DAAFEKRYRV DLLNTDHTLD PSLLESGSEI LGDLKLQVLL DEEYKQLVKD RKFLREVFVD GEANWPLPVN I RRIIQNAQ QTFHIDHTKP SDLTIKDIVL GVKDLQENLL VLRGKNEIIQ NAQRDAVTLF CCLLRSRLAT RRVLQEYRLT KQ AFDWVLS NIEAQFLRSV VHPGEMVGVL AAQSIGEPAT QMTLNTFHFA GVASKKVTSG VPRLKEILNV AKNMKTPSLT VYL EPGHAA DQEQAKLIRS AIEHTTLKSV TIASEIYYDP DPRSTVIPED EEIIQLHFSL LDEEAEQSFD QQSPWLLRLE LDRA AMNDK DLTMGQVGER IKQTFKNDLF VIWSEDNDEK LIIRCRVVRP KSLDAETEAE EDHMLKKIEN TMLENITLRG VENIE RVVM MKYDRKVPSP TGEYVKEPEW VLETDGVNLS EVMTVPGIDP TRIYTNSFID IMEVLGIEAG RAALYKEVYN VIASDG SYV NYRHMALLVD VMTTQGGLTS VTRHGFNRSN TGALMRCSFE ETVEILFEAG ASAELDDCRG VSENVILGQM APIGTGA FD VMIDEESLVK YMPEQKITEI EDGQDGGVTP YSNESGLVNA DLDVKDELMF SPLVDSGSND AMAGGFTAYG GADYGEAT S PFGAYGEAPT SPGFGVSSPG FSPTSPTYSP TSPAYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP SYSPTSPSY SPTSPNYSPT SPSYSPTSPG YSPGSPAYSP KQDEQKHNEN ENSR

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

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Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 2
Details: Residues (1225B-1259B) are an affinity tag(containing a TEV-6xHis-3xFlag tag) we modified in the genome of target strain for convenient protein purification.
Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 143.336766 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG ...String:
MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG RLPIMLRSKN CYLSEATESD LYKLKECPFD MGGYFIINGS EKVLIAQERS AGNIVQVFKK AAPSPISHVA EI RSALEKG SRFISTLQVK LYGREGSSAR TIKATLPYIK QDIPIVIIFR ALGIIPDGEI LEHICYDVND WQMLEMLKPC VED GFVIQD RETALDFIGR RGTALGIKKE KRIQYAKDIL QKEFLPHITQ LEGFESRKAF FLGYMINRLL LCALDRKDQD DRDH FGKKR LDLAGPLLAQ LFKTLFKKLT KDIFRYMQRT VEEAHDFNMK LAINAKTITS GLKYALATGN WGEQKKAMSS RAGVS QVLN RYTYSSTLSH LRRTNTPIGR DGKLAKPRQL HNTHWGLVCP AETPEGQACG LVKNLSLMSC ISVGTDPMPI ITFLSE WGM EPLEDYVPHQ SPDATRVFVN GVWHGVHRNP ARLMETLRTL RRKGDINPEV SMIRDIREKE LKIFTDAGRV YRPLFIV ED DESLGHKELK VRKGHIAKLM ATEYQDIEGG FEDVEEYTWS SLLNEGLVEY IDAEEEESIL IAMQPEDLEP AEANEEND L DVDPAKRIRV SHHATTFTHC EIHPSMILGV AASIIPFPDH NQSPRNTYQS AMGKQAMGVF LTNYNVRMDT MANILYYPQ KPLGTTRAME YLKFRELPAG QNAIVAIACY SGYNQEDSMI MNQSSIDRGL FRSLFFRSYM DQEKKYGMSI TETFEKPQRT NTLRMKHGT YDKLDDDGLI APGVRVSGED VIIGKTTPIS PDEEELGQRT AYHSKRDAST PLRSTENGIV DQVLVTTNQD G LKFVKVRV RTTKIPQIGD KFASRHGQKG TIGITYRRED MPFTAEGIVP DLIINPHAIP SRMTVAHLIE CLLSKVAALS GN EGDASPF TDITVEGISK LLREHGYQSR GFEVMYNGHT GKKLMAQIFF GPTYYQRLRH MVDDKIHARA RGPMQVLTRQ PVE GRSRDG GLRFGEMERD CMIAHGAASF LKERLMEASD AFRVHICGIC GLMTVIAKLN HNQFECKGCD NKIDIYQIHI PYAA KLLFQ ELMAMNITPR LYTDRSRDFE NLYFQGHHHH HHDYKDHDGD YKDHDIDYKD DDDK

UniProtKB: DNA-directed RNA polymerase II subunit RPB2

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Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 35.330457 KDa
SequenceString: MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA ...String:
MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA KWGPAAAIEF EYDPWNKLKH TDYWYEQDSA KEWPQSKNCE YEDPPNEGDP FDYKAQADTF YMNVESVGSI PV DQVVVRG IDTLQKKVAS ILLALTQMDQ DKVNFASGDN NTASNMLGSN EDVMMTGAEQ DPYSNASQMG NTGSGGYDNA W

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

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Macromolecule #4: DNA-directed RNA polymerase II subunit RPB4

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 25.451191 KDa
SequenceString: MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK EALVERRRAF KRSQKKHKKK HLKHENAND ETTAVEDEDD DLDEDDVNAD DDDFMHSETR EKELESIDVL LEQTTGGNNK DLKNTMQYLT NFSRFRDQET V GAVIQLLK ...String:
MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK EALVERRRAF KRSQKKHKKK HLKHENAND ETTAVEDEDD DLDEDDVNAD DDDFMHSETR EKELESIDVL LEQTTGGNNK DLKNTMQYLT NFSRFRDQET V GAVIQLLK STGLHPFEVA QLGSLACDTA DEAKTLIPSL NNKISDDELE RILKELSNLE TLY

UniProtKB: DNA-directed RNA polymerase II subunit RPB4

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Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 25.117094 KDa
SequenceString: MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY ...String:
MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY RLKESQLPRI QRADPVALYL GLKRGEVVKI IRKSETSGRY ASYRICM

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

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Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 17.931834 KDa
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTLK EKAIPKDQRA TTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR IAMKELAEKK IPLVIRRYLP DGSFEDWSVE ELIVDL

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

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Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 19.081053 KDa
SequenceString:
MFFIKDLSLN ITLHPSFFGP RMKQYLKTKL LEEVEGSCTG KFGYILCVLD YDNIDIQRGR ILPTDGSAEF NVKYRAVVFK PFKGEVVDG TVVSCSQHGF EVQVGPMKVF VTKHLMPQDL TFNAGSNPPS YQSSEDVITI KSRIRVKIEG CISQVSSIHA I GSIKEDYL GAI

UniProtKB: DNA-directed RNA polymerase II subunit RPB7

+
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: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 16.525363 KDa
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTPA NDSSATRSWR PPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG GLLMRLEGNY RNLNNLKQEN AYLLIRR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

+
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: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 14.308161 KDa
SequenceString:
MTTFRFCRDC NNMLYPREDK ENNRLLFECR TCSYVEEAGS PLVYRHELIT NIGETAGVVQ DIGSDPTLPR SDRECPKCHS RENVFFQSQ QRRKDTSMVL FFVCLSCSHI FTSDQKNKRT QFS

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 8.290732 KDa
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKRD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

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Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 13.633493 KDa
SequenceString:
MNAPDRFELF LLGEGESKLK IDPDTKAPNA VVITFEKEDH TLGNLIRAEL LNDRKVLFAA YKVEHPFFAR FKLRIQTTEG YDPKDALKN ACNSIINKLG ALKTNFETEW NLQTLAADDA F

UniProtKB: DNA-directed RNA polymerase II subunit RPB11

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Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 7.729969 KDa
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

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Macromolecule #13: 5'-3' exoribonuclease 2

MacromoleculeName: 5'-3' exoribonuclease 2 / type: protein_or_peptide / ID: 13
Details: Residues (1M-13M) are also an affinity tag for convenient protein purification.
Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 117.606508 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDMGVPSFF RWLSRKYPKI ISPVLEEQPQ IVDGVILPLD YSASNPNGEL DNLYLDMNGI VHPCSHPENK PPPETEDEM LLAVFEYTNR VLNMARPRKV LVMAVDGVAP RAKMNQQRAR RFRSARDAQI ENEAREEIMR QREEVGEIID D AVRNKKTW ...String:
MGSSHHHHHH SQDMGVPSFF RWLSRKYPKI ISPVLEEQPQ IVDGVILPLD YSASNPNGEL DNLYLDMNGI VHPCSHPENK PPPETEDEM LLAVFEYTNR VLNMARPRKV LVMAVDGVAP RAKMNQQRAR RFRSARDAQI ENEAREEIMR QREEVGEIID D AVRNKKTW DSNAITPGTP FMDKLAAALR YWTAFKLATD PGWKNLQVII SDATVPGEGE HKIMNFIRSQ RADPEYNPNT TH CIYGLDA DLIFLGLATH EPHFKILRED VFAQDNRKRN NLKDTINMTE EEKQFLQKQN SEQPFLWLHI NVLREYLSAE LWV PGLPFT FDLERAIDDW VFMCFFCGND FLPHLPCLDV RENSIDILLD IWKVVLPKLK TYMTCDGVLN LPSVETLLQH LGSR EGDIF KTRHIQEARK KEAFERRKAQ KNMSKGQDRH PTVATEQLQM YDTQGNLAKG SWNLTTSDMV RLKKELMLAN EGNEE AIAK VKQQSDKNNE LMKDISKEEI DDAVSKANKT NFNLAEVMKQ KIINKKHRLE KDNEEEEIAK DSKKVKTEKA ESECDL DAE IKDEIVADVN DRENSETTEV SRDSPVHSTV NVSEGPKNGV FDTDEFVKLF EPGYHERYYT AKFHVTPQDI EQLRKDM VK CYIEGVAWVL MYYYQGCASW NWFYPYHYAP LATDFHGFSH LEIKFEEGTP FLPYEQLMSV LPAASGHALP KIFRSLMS E PDSEIIDFYP EEFPIDMNGK KMSWQGIALL PFIDQDRLLT AVRAQYPLLS DAERARNIRG EPVLLISNKN ANYERFSKK LYSKENNNNN VVVKFQHFKS GLSGIVSKDV EGFELNGKIV CPIQGGSLPN LSTTLILKMS YRLIPLPSRN KSIILNGFIP SEPVLTAYD LDSIMYKYNN QNYSRRWNFG NDLKQNIVPV GPKGITQYKP RTGGYRAFFY FAELSRNNVQ PAHNYGRNSY N SQPGFNNS RYDGGNNNYR QNSNYRNNNY SGNRNSGQYS GNSYSRNNKQ SRYDNSRANR R

UniProtKB: 5'-3' exoribonuclease 2

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Macromolecule #15: Decapping nuclease RAI1

MacromoleculeName: Decapping nuclease RAI1 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 44.571445 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGVSANLFVK QRGSTTALKQ PKEIGFYSRT KDEEYLISDD TNLNYYYLPD AELDRKLDLS SGFQKFKDYY KDFEDRCSLR GLLETIESS ERHKGKKINA DIITFRGIAR KLISCAFDSP SFNTVDLRIV SFNGQLFIKE VPEAVNAAKA SSATEAGRNI N QDLNVFTG ...String:
MGVSANLFVK QRGSTTALKQ PKEIGFYSRT KDEEYLISDD TNLNYYYLPD AELDRKLDLS SGFQKFKDYY KDFEDRCSLR GLLETIESS ERHKGKKINA DIITFRGIAR KLISCAFDSP SFNTVDLRIV SFNGQLFIKE VPEAVNAAKA SSATEAGRNI N QDLNVFTG YKFETLATLS NPLQYTPREV IEKRTKRIVS HGDEYISVVR TGVGNCKLIL GAEVDCIFDF KENGRDNLKH YA ELKCTQQ VANISDTHKF ERKLFRTWLQ CFLVGIPRII YGFKDDHYVL KTVEEFSTEE VPVLLKNNNP QVGSACLEAI KWY GLLTEW LLKMIPRDED PHSQIRAFKL VFENNHLRLS EIEESDEEYS GLIDGEHILS NGFKEWRKSL K

UniProtKB: Decapping nuclease RAI1

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Macromolecule #18: Transcription elongation factor SPT5

MacromoleculeName: Transcription elongation factor SPT5 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 115.797969 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSDNSDTNVS MQDHDQQFAD PVVVPQSTDT KDENTSDKDT VDSGNVTTTE STERAESTSN IPPLDGEEKE AKSEPQQPED NAETAATEQ VSSSNGPATD DAQATLNTDS SEANEIVKKE EGSDERKRPR EEDTKNSDGD TKDEGDNKDE DDDEDDDDDD D DEDDDDEA ...String:
MSDNSDTNVS MQDHDQQFAD PVVVPQSTDT KDENTSDKDT VDSGNVTTTE STERAESTSN IPPLDGEEKE AKSEPQQPED NAETAATEQ VSSSNGPATD DAQATLNTDS SEANEIVKKE EGSDERKRPR EEDTKNSDGD TKDEGDNKDE DDDEDDDDDD D DEDDDDEA PTKRRRQERN RFLDIEAEVS DDEDEDEDEE DSELVREGFI THGDDEDDEA SAPGARRDDR LHRQLDQDLN KT SEEDAQR LAKELRERYG RSSSKQYRAA AQDGYVPQRF LLPSVDTATI WGVRCRPGKE KELIRKLLKK KFNLDRAMGK KKL KILSIF QRDNYTGRIY IEAPKQSVIE KFCNGVPDIY ISQKLLIPVQ ELPLLLKPNK SDDVALEEGS YVRIKRGIYK GDLA MVDQI SENNLEVMLK IVPRLDYGKF DEIDPTTQQR KSRRPTFAHR APPQLFNPTM ALRLDQANLY KRDDRHFTYK NEDYI DGYL YKSFRIQHVE TKNIQPTVEE LARFGSKEGA VDLTSVSQSI KKAQAAKVTF QPGDRIEVLN GEQRGSKGIV TRTTKD IAT IKLNGFTTPL EFPISTLRKI FEPGDHVTVI NGEHQGDAGL VLMVEQGQVT FMSTQTSREV TITANNLSKS IDTTATS SE YALHDIVELS AKNVACIIQA GHDIFKVIDE TGKVSTITKG SILSKINTAR ARVSSVDANG NEIKIGDTIV EKVGSRRE G QVLYIQTQQI FVVSKKIVEN AGVFVVNPSN VEAVASKDNM LSNKMDLSKM NPEIISKMGP PSSKTFQQPI QSRGGREVA LGKTVRIRSA GYKGQLGIVK DVNGDKATVE LHSKNKHITI DKHKLTYYNR EGGEGITYDE LVNRRGRVPQ ARMGPSYVSA PRNMATGGI AAGAAATSSG LSGGMTPGWS SFDGGKTPAV NAHGGSGGGG VSSWGGASTW GGQGNGGASA WGGAGGGASA W GGQGTGAT STWGGASAWG NKSSWGGAST WASGGESNGA MSTWGGTGDR SAYGGASTWG GNNNNKSTRD GGASAWGNQD DG NRSAWNN QGNKSNYGGN STWGGH

UniProtKB: Transcription elongation factor SPT5

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Macromolecule #14: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.892528 KDa
SequenceString:
(DC)(DC)(DG)(DT)(DG)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DT)(DA)(DA)(DA) (DT)(DG)(DG)(DT)(DT)(DT)(DG)(DT)(DG) (DT)(DC)(DT)(DG)(DC)(DT)(DT)(DA)(DT)(DC) (DG) (DG)(DT)(DA)(DG)(DA)(DG)(DT)(DG)

+
Macromolecule #17: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 17 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.658418 KDa
SequenceString:
(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DC)(DC)(DG) (DA)(DT)(DA)(DA)(DG)(DC)(DA)(DG)(DA)(DC) (DA)(DT)(DA)(DC)(DC)(DT)(DC)(DT)(DC) (DG)(DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DC) (DT) (DA)(DG)(DA)(DC)(DA)(DC)(DG)(DG)

+
Macromolecule #16: RNA

MacromoleculeName: RNA / type: rna / ID: 16 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.403457 KDa
SequenceString:
ACAGAUCGUG UCCAUCGAGA GGU

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Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #20: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 20 / Number of copies: 3 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 0.01 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5vvs

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 416223
FSC plot (resolution estimation)

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