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- EMDB-42502: Cyanobacterial RNA polymerase elongation complex with NusG and CTP -

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Basic information

Entry
Database: EMDB / ID: EMD-42502
TitleCyanobacterial RNA polymerase elongation complex with NusG and CTP
Map data
Sample
  • Complex: Cyanobacterial RNA polymerase elongation complex with NusG and CTP
    • Protein or peptide: x 6 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 3 types
KeywordsTranscription regulation / RNAP / NusG / cryo-EM / TRANSCRIPTION
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription ...transcription elongation-coupled chromatin remodeling / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase, subunit gamma / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / NusG, N-terminal ...DNA-directed RNA polymerase, subunit gamma / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / 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, omega subunit / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW / KOW motif / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit gamma / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsQayyum MZ / Imashimizu M / Leanca M / Vishwakarma RK / Bradley Riaz A / Yuzenkova Y / Murakami KS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131860 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase.
Authors: M Zuhaib Qayyum / Masahiko Imashimizu / Miron Leanca / Rishi K Vishwakarma / Amber Riaz-Bradley / Yulia Yuzenkova / Katsuhiko S Murakami /
Abstract: Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish them from canonical bacterial RNAPs. The largest ...Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish them from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β'1 and β'2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spanning approximately half of the β'2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP in the absence of iNTP bound at the active site and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG, or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms and organelle.
History
DepositionOct 26, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42502.png

Downloads & links

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Map

FileDownload / File: emd_42502.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.855 Å
Density
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-0.5533021 - 1.2891798
Average (Standard dev.)0.00033892586 (±0.03523864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42502_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42502_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cyanobacterial RNA polymerase elongation complex with NusG and CTP

EntireName: Cyanobacterial RNA polymerase elongation complex with NusG and CTP
Components
  • Complex: Cyanobacterial RNA polymerase elongation complex with NusG and CTP
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit gammaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • Protein or peptide: Transcription termination/antitermination protein NusG
    • DNA: DNA (40-MER)
    • DNA: DNA (40-MER)
    • RNA: RNA (5'-R(P*AP*AP*AP*GP*AP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: CYTIDINE-5'-TRIPHOSPHATE

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Supramolecule #1: Cyanobacterial RNA polymerase elongation complex with NusG and CTP

SupramoleculeName: Cyanobacterial RNA polymerase elongation complex with NusG and CTP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Synechococcus elongatus (bacteria)

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Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 33.814891 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTFQVECVES RTEADQGQYG RFSIEPLARG QGTTVGNALR RVLLSNLEGT AVTAVRIGGV NHEFATIPGV REDVLDILLN VRELVVHAH SPQPQIGRLR VVGPATVTAA DVDFGPEVEV INPNHYIASL SEGATLEMEL KVEWGTGYRA IDRSHDETTA L DFLQLDAV ...String:
MTFQVECVES RTEADQGQYG RFSIEPLARG QGTTVGNALR RVLLSNLEGT AVTAVRIGGV NHEFATIPGV REDVLDILLN VRELVVHAH SPQPQIGRLR VVGPATVTAA DVDFGPEVEV INPNHYIASL SEGATLEMEL KVEWGTGYRA IDRSHDETTA L DFLQLDAV FMPVRRVNYS VEDARVGEST AIDRLVLEVW TNGSLSPQEA LSQAASCLVA LFEPLKNVSV GSTHTADPEP TP ESQTPIE DLQLSVRAYN CLKRAQVNSV ADLLSYTYED LLEIKNFGQK SAEEVVEALE RIGIKLQESK VS

UniProtKB: DNA-directed RNA polymerase subunit alpha

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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: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 123.428547 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEQTQLAPA AFHLPDLVAI QRNSFRWFLE EGLIEELESF SPITDYTGKL ELHFLGKQYK LKRPKYDVDE AKRRDGTYSV QMYVPTRLI NKETGEIKEQ EVFIGDLPLM TDRGTFIING AERVIVNQIV RSPGVYYKSE RDKNGRLTHN ASLIPNRGAW L KFETDKNG ...String:
MAEQTQLAPA AFHLPDLVAI QRNSFRWFLE EGLIEELESF SPITDYTGKL ELHFLGKQYK LKRPKYDVDE AKRRDGTYSV QMYVPTRLI NKETGEIKEQ EVFIGDLPLM TDRGTFIING AERVIVNQIV RSPGVYYKSE RDKNGRLTHN ASLIPNRGAW L KFETDKNG LVWVRIDKTR KLSAQVLLKA LGLSDNEIYD KLRHPEYYQK TIDKEGQFSE DEALMELYRK LRPGEPPTVS GG QQLLESR FFDPKRYDLG RVGRYKLNKK LGLNVADTVR TLTSEDILAA IDYLINLELD LGGCEVDDID HLGNRRVRSV GEL LQNQVR VGLNRLERII RERMTVSDSD SLSPASLVNP KPLVAAIKEF FGSSQLSQFM DQTNPLAELT HKRRLSALGP GGLT RERAG FAVRDIHPSH YGRICPIETP EGPNAGLIGS LATHARVNDY GFIETPFWRV EEGRVRKDLA PVYMTADQED DLRVA PGDV ATDDAGYILG TTIPVRYRQD FTTTTPERVD YVALSPVQII SVATSLIPFL EHDDANRALM GSNMQRQAVP LLRPER PLV GTGLEPQAAR DSGMVITSPV DGTISYVDAT HIEVTADTGE KYGYALQKYQ RSNQDTCLNQ RPIVFEGDRV QRGQVIA DG SATEKGELAL GQNILVAYMP WEGYNYEDAI LISERLVYDD VYTSIHIEKF EIEARQTKLG PEEITREIPN VGEDALRQ L DENGIIRVGA WVESGDILVG KVTPKGESDQ PPEEKLLRAI FGEKARDVRD NSLRVPNGEK GRVVDVRLFT REQGDELPP GANMVVRVYV AQKRKIQVGD KMAGRHGNKG IISRILPCED MPYLPDGTPL DIVLNPLGVP SRMNVGQVFE CMLGWAGQLL DARFKVTPF DEMYGAEASR LTVNAKLSEA REQTGQPWVF SDDEPGKIQV YDGRTGEPFD RPVTVGRAYM LKLVHLVDDK I HARSTGPY SLVTQQPLGG KAQQGGQRFG EMEVWALEAY GAAYILQELL TVKSDDMQGR NEALNAIVKG KAIPRPGTPE SF KVLMREL QSLCLDIAVY KASTEDYEED KEVDLMADVN QRRTPSRPTY ESMSVGDIDD DDD

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit gamma

MacromoleculeName: DNA-directed RNA polymerase subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 71.054367 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAKQEQRFDY VKIALASPER IRQWGERTLP NGQVVGEVTK PETINYRTLK PEMDGLFCEK IFGPAKDWEC HCGKYKRVRH RGIVCERCG VEVTESRVRR HRMGFIKLAA PVAHVWYLKG IPSYIAILLD MPLRDVEQIV YFNSYVVLNP GNHSELQYKQ L LNEDQWME ...String:
MAKQEQRFDY VKIALASPER IRQWGERTLP NGQVVGEVTK PETINYRTLK PEMDGLFCEK IFGPAKDWEC HCGKYKRVRH RGIVCERCG VEVTESRVRR HRMGFIKLAA PVAHVWYLKG IPSYIAILLD MPLRDVEQIV YFNSYVVLNP GNHSELQYKQ L LNEDQWME IEDQIYAEES DLEGIEVGIG AEALQQLLQD LNLNEESEKL RQEIAESKGQ KRAKLIKRLR VIDNFIGTES RP EWMVLNV IPVIPPDLRP MVQLDGGRFA TSDLNDLYRR VINRNNRLAR LQEILAPEII VRNEKRMLQE AVDALIDNGR RGR TVVGAN NRPLKSLSDI IEGKQGRFRQ NLLGKRVDYS GRSVIVVGPN LKIHQCGLPR EMAIELFQPF VIHRLIKNHS INNI KQAKK LIQKNDPLIW DVLEEVIEGH PVMLNRAPTL HRLGIQAFEP ILVEGRAIQL HPLVCPAFNA DFDGDQMAVH VPLSI EAQA EARMLMLASG NILSPATGQP IVTPSQDMVL GCYYLTAENP GAQKGAGRYF ANLEDAIRAF EQGSVDLHAW VWVRFD GEV ESEGESDEPE SVVAADDGTV TKTYRFRRIR ETEDGQRLSQ YVKTTPGRIL FNNTVQTALI H

UniProtKB: DNA-directed RNA polymerase subunit gamma

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Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 8.787966 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MLQRFDLDSQ DLLFKAESLI VNSTNRYHVT LQIARRAKQA RYEEMENLSE ETGIKPVLRA ILEMSDELNQ PEIIGG

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 144.006031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEAKSAPIF RNRVIDKKQL KKLIGWTFAH YGTAKTAVVA DDLKALGFRY ATRAGVSISI DDLKVPGSKA ELLESAEKRI QETEDRYTR GEITEVERFQ KVIDTWANTN DELTDRVVKN FRESDPLNSV YMMAFSGARG NISQVRQLVG MRGLMANPQG E IIDLPIKT ...String:
MAEAKSAPIF RNRVIDKKQL KKLIGWTFAH YGTAKTAVVA DDLKALGFRY ATRAGVSISI DDLKVPGSKA ELLESAEKRI QETEDRYTR GEITEVERFQ KVIDTWANTN DELTDRVVKN FRESDPLNSV YMMAFSGARG NISQVRQLVG MRGLMANPQG E IIDLPIKT NFREGLTVTE YIISSYGARK GLVDTALRTA DSGYLTRRLV DVSQDVIIHE VDCGTSRGLF VEAMTDGDRI LI PISQRLL GRVTAEAVLD PSTDEVLAEA GQDINEDLAN RIEKAGIKKV KVRSPLTCEA ARSVCQKCYG WSLAHAQMVD MGE AVGIIA AQSIGEPGTQ LTMRTFHTGG VFTGETARLL RAPVAGTIKL GKKARTRPYR TRHGEEALLA EANFDLVLEG KGRK ETFAI LQGSTIFVQD GDKVAAEAIL AEVPVSGRTK RTVEKATKDV ATDLAGEIRF QDIVPEEKTD RQGNTTRIAQ RGGLL WVLA GDVYNLLPGA EPTVKNGDRV EVGDVLAETK LTTERGGTVR MGEDNGSSTH REVEIITASV VLDTATVKAE ASQGRE HYV IETKGGQRFN LLAAPGTKVT TGHVVAELID SRYRTQTGGL LKYSGVEISK KGRAKAKQGY EVTKGGTLLW IPEETHE VN KDISLLNVED GQLVEAGTEV VKDIFCQTTG IVSVTQNNDI LREIVIKPGD VHVLDDPDTA AKYDEGRLVN AGEEVFPG L TAEQLVWAEA VDGTDGPLLL LRPVQELVIP DEPPVPSQDS SQESSSRSIR LRAVQRLQFQ DGERIKSVEG VDLLRTQLV LESEEGSSQL SADIELLPDS KDPETLRLQL VIIEPVVIRR DVASDTTHGS THTELRVKDG QKVKPGAVIA CTQIQCKEAG VVRGIQEGS EAVRRLLVER ERDCVTLDLD VTAATQLQPG SLIVAGTQLV DGIIAPESGE VRAIAPGQLQ LRIARPYRVS Q GAVLHVED KGLVQRGDNL VLLVFERAKT GDIIQGLPRI EELLEARKPK EACILARRPG VAHINYSDDD AIDIQVIEAD GT QADYPVG PGQPLIISDG ETVDAGQALT DGPANPHDLL EIYYDYFREQ LGEDYEAALE SLRRVQALLV NEVQSVYQSQ GID ISDKHI EVIVRQMTSK VRIDDGGDTI MLPGELHELR EVYNSNNTMA LTGMAPAQFT PVLLGITKAS LNTNSFISAA SFQE TTRVL TEAAIEGKSD WLRGLKENVI IGRLIPAGTG FKAYEESLLT DVDGGYEDRV YDDDLADVVI DDRAARSYTL NEGRD FSRS MTFAEGESMI LDDGEELIDD SSASLRNLVD VDED

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #6: Transcription termination/antitermination protein NusG

MacromoleculeName: Transcription termination/antitermination protein NusG
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 23.117375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTDQYEEQLL SADDSVASEK ARWYAVQVAS GCEKRVKATL EQRVQTLDAA NRILQVEIPE TPIVKLKKDG SRQSAEEKVF PGYVLVRMI LDDDAWQIVR NTPHVINFVG AEQKRPYGRG RGHVKPMPLS PGEVGRIFKR AQEQKPTVKI DLAEGDQILV L SGPFKDFE ...String:
MTDQYEEQLL SADDSVASEK ARWYAVQVAS GCEKRVKATL EQRVQTLDAA NRILQVEIPE TPIVKLKKDG SRQSAEEKVF PGYVLVRMI LDDDAWQIVR NTPHVINFVG AEQKRPYGRG RGHVKPMPLS PGEVGRIFKR AQEQKPTVKI DLAEGDQILV L SGPFKDFE GTVIEVSPER SKLKALLSIF GRDTPVELEF NQVQKQN

UniProtKB: Transcription termination/antitermination protein NusG

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Macromolecule #7: DNA (40-MER)

MacromoleculeName: DNA (40-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.380916 KDa
SequenceString:
(DG)(DG)(DG)(DC)(DG)(DC)(DA)(DT)(DG)(DC) (DT)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DG)(DA) (DG)(DA)(DG)(DG)(DT)(DA)(DC)(DA)(DC) (DG)(DG)(DC)(DG)(DA)(DC)(DT)(DG)(DC)(DC) (DC)

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Macromolecule #8: DNA (40-MER)

MacromoleculeName: DNA (40-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.251828 KDa
SequenceString:
(DG)(DG)(DG)(DC)(DA)(DG)(DT)(DC)(DG)(DC) (DC)(DG)(DT)(DG)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DT)(DA)(DG)(DA)(DG)(DC) (DA)(DG)(DC)(DA)(DT)(DG)(DC)(DG)(DC)(DC) (DC)

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Macromolecule #9: RNA (5'-R(P*AP*AP*AP*GP*AP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*GP*AP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
type: rna / ID: 9 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.863198 KDa
SequenceString:
AGCAUUCAAA GAGGAGAGGU A

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #12: CYTIDINE-5'-TRIPHOSPHATE

MacromoleculeName: CYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 1 / Formula: CTP
Molecular weightTheoretical: 483.156 Da
Chemical component information

ChemComp-CTP:
CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate

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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: 8 / Details: 40mM Tris-HCl 200mM KCl 1mM EDTA 1mM DTT 5mM MgCl2
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: OTHER / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 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:

8syi

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132172

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