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- EMDB-4888: Structure of the core Vaccinia Virus DNA-dependent RNA polymerase... -

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Basic information

Entry
Database: EMDB / ID: EMD-4888
TitleStructure of the core Vaccinia Virus DNA-dependent RNA polymerase complex
Map dataPost-processed map used for building.
Sample
  • Complex: Core Vaccinia DNA-dependent RNA polymerase complex
    • Complex: DNA-dependent RNA polymerase subunitsRNA polymerase
      • Protein or peptide: x 9 types
  • Ligand: x 2 types
Function / homology
Function and homology information


virion component => GO:0044423 / viral transcription / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-binding transcription factor activity / DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
RNA polymerase-associated transcription specificity factor Rap94 / RNA polymerase-associated transcription specificity factor, Rap94 / DNA-directed RNA polymerase, 18kDa subunit, poxviral / DNA-directed RNA polymerase, 35kDa subunit, poxviral / RNA polymerase, 22kDa subunit, poxviral / DNA-directed RNA polymerase, 19kDa subunit, poxviral / DNA-directed RNA polymerase, 7kDa polypeptide, chordopoxviral / RNA polymerase, 30kDa subunit, chordopox-type / RNA polymerase, 132kDa subunit, poxvirus-type / RNA polymerase, 30kDa subunit, chordopox-type, N-terminal ...RNA polymerase-associated transcription specificity factor Rap94 / RNA polymerase-associated transcription specificity factor, Rap94 / DNA-directed RNA polymerase, 18kDa subunit, poxviral / DNA-directed RNA polymerase, 35kDa subunit, poxviral / RNA polymerase, 22kDa subunit, poxviral / DNA-directed RNA polymerase, 19kDa subunit, poxviral / DNA-directed RNA polymerase, 7kDa polypeptide, chordopoxviral / RNA polymerase, 30kDa subunit, chordopox-type / RNA polymerase, 132kDa subunit, poxvirus-type / RNA polymerase, 30kDa subunit, chordopox-type, N-terminal / Poxvirus DNA-directed RNA polymerase, 18 kD subunit / Poxvirus DNA-directed RNA polymerase, 35 kD subunit / Poxvirus RNA polymerase 22 kDa subunit / Poxvirus DNA-directed RNA polymerase 19 kDa subunit / Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7) / Poxvirus DNA dependent RNA polymerase 30kDa subunit / Poxvirus DNA dependent RNA polymerase / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / 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, 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
Similarity search - Domain/homology
DNA-directed RNA polymerase 30 kDa polypeptide / DNA-directed RNA polymerase 7 kDa subunit / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase 147 kDa polypeptide / Protein H4 / DNA-directed RNA polymerase 18 kDa subunit / DNA-directed RNA polymerase 19 kDa subunit / DNA-directed RNA polymerase / DNA-directed RNA polymerase 35 kDa subunit
Similarity search - Component
Biological speciesVaccinia virus GLV-1h68
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGrimm C / Hillen HS / Bedenk K / Bartuli J / Neyer S / Zhang Q / Huettenhofer A / Erlacher M / Dienemann C / Schlosser A ...Grimm C / Hillen HS / Bedenk K / Bartuli J / Neyer S / Zhang Q / Huettenhofer A / Erlacher M / Dienemann C / Schlosser A / Urlaub H / Boettcher B / Szalay A / Cramer P / Fischer U
Funding support Germany, 7 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
German Federal Ministry for Education and ResearchEXC 2067/1- 390729940 Germany
German Research Foundation (DFG)SPP1935 Germany
Volkswagen Foundation Germany
European Research Council (ERC)TRANSREGULON Germany
German Research Foundation (DFG)Fi 573 18-1 Germany
German Research Foundation (DFG)Fi 573 7-2 Germany
CitationJournal: Cell / Year: 2019
Title: Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes.
Authors: Hauke S Hillen / Julia Bartuli / Clemens Grimm / Christian Dienemann / Kristina Bedenk / Aladar A Szalay / Utz Fischer / Patrick Cramer /
Abstract: Poxviruses use virus-encoded multisubunit RNA polymerases (vRNAPs) and RNA-processing factors to generate mG-capped mRNAs in the host cytoplasm. In the accompanying paper, we report structures of ...Poxviruses use virus-encoded multisubunit RNA polymerases (vRNAPs) and RNA-processing factors to generate mG-capped mRNAs in the host cytoplasm. In the accompanying paper, we report structures of core and complete vRNAP complexes of the prototypic Vaccinia poxvirus (Grimm et al., 2019; in this issue of Cell). Here, we present the cryo-electron microscopy (cryo-EM) structures of Vaccinia vRNAP in the form of a transcribing elongation complex and in the form of a co-transcriptional capping complex that contains the viral capping enzyme (CE). The trifunctional CE forms two mobile modules that bind the polymerase surface around the RNA exit tunnel. RNA extends from the vRNAP active site through this tunnel and into the active site of the CE triphosphatase. Structural comparisons suggest that growing RNA triggers large-scale rearrangements on the surface of the transcription machinery during the transition from transcription initiation to RNA capping and elongation. Our structures unravel the basis for synthesis and co-transcriptional modification of poxvirus RNA.
History
DepositionApr 23, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseDec 18, 2019-
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: 0.0275
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0275
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ric
  • Surface level: 0.0275
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4888.png

Downloads & links

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Map

FileDownload / File: emd_4888.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed map used for building.
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 0.0275 / Movie #1: 0.0275
Minimum - Maximum-0.091687046 - 0.16102602
Average (Standard dev.)0.00041528157 (±0.005382401)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z243.000243.000243.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0920.1610.000

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Supplemental data

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Mask #1

Fileemd_4888_msk_1.map
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Mask #2

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Mask #3

Fileemd_4888_msk_3.map
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Mask #4

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Additional map: Rap94 CTD focused 3D refinement half-map 1.

Fileemd_4888_additional_1.map
AnnotationRap94 CTD focused 3D refinement half-map 1.
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Additional map: Rpo30 focused 3D refinement post-processed map.

Fileemd_4888_additional_10.map
AnnotationRpo30 focused 3D refinement post-processed map.
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Additional map: Rap94 Domain2 focused 3D refinement map.

Fileemd_4888_additional_11.map
AnnotationRap94 Domain2 focused 3D refinement map.
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Additional map: Rap94 CTD focused 3D refinement map.

Fileemd_4888_additional_12.map
AnnotationRap94 CTD focused 3D refinement map.
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Additional map: Global 3D refinement map.

Fileemd_4888_additional_13.map
AnnotationGlobal 3D refinement map.
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Additional map: Composite map used for real space refinement.

Fileemd_4888_additional_14.map
AnnotationComposite map used for real space refinement.
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Additional map: Rap94 CTD focused 3D refinement half-map 1.

Fileemd_4888_additional_2.map
AnnotationRap94 CTD focused 3D refinement half-map 1.
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Additional map: Rap94 Domain2 focused 3D refinement half-map 2.

Fileemd_4888_additional_3.map
AnnotationRap94 Domain2 focused 3D refinement half-map 2.
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Additional map: Rap94 Domain2 focused 3D refinement half-map 1.

Fileemd_4888_additional_4.map
AnnotationRap94 Domain2 focused 3D refinement half-map 1.
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Additional map: Rap94 Domain2 focused 3D refinement post-processed map.

Fileemd_4888_additional_5.map
AnnotationRap94 Domain2 focused 3D refinement post-processed map.
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Additional map: Rap94 CTD focused 3D refinement post-processed map.

Fileemd_4888_additional_6.map
AnnotationRap94 CTD focused 3D refinement post-processed map.
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Additional map: Rpo30 focused 3D refinement map.

Fileemd_4888_additional_7.map
AnnotationRpo30 focused 3D refinement map.
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Additional map: Rpo30 focused 3D refinement half-map 1.

Fileemd_4888_additional_8.map
AnnotationRpo30 focused 3D refinement half-map 1.
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Additional map: Rpo30 focused 3D refinement half-map 2.

Fileemd_4888_additional_9.map
AnnotationRpo30 focused 3D refinement half-map 2.
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Half map: Global 3D refinement half-map 2.

Fileemd_4888_half_map_1.map
AnnotationGlobal 3D refinement half-map 2.
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Half map: Global 3D refinement half-map 1.

Fileemd_4888_half_map_2.map
AnnotationGlobal 3D refinement half-map 1.
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Sample components

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Entire : Core Vaccinia DNA-dependent RNA polymerase complex

EntireName: Core Vaccinia DNA-dependent RNA polymerase complex
Components
  • Complex: Core Vaccinia DNA-dependent RNA polymerase complex
    • Complex: DNA-dependent RNA polymerase subunitsRNA polymerase
      • Protein or peptide: DNA-dependent RNA polymerase subunit rpo147RNA polymerase
      • Protein or peptide: DNA-dependent RNA polymerase subunit rpo132RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase 35 kDa subunit
      • Protein or peptide: DNA-directed RNA polymerase subunitPolymerase
      • Protein or peptide: DNA-directed RNA polymerase 19 kDa subunit
      • Protein or peptide: DNA-dependent RNA polymerase subunit rpo18RNA polymerase
      • Protein or peptide: RAP94 transcription factor
      • Protein or peptide: DNA-dependent RNA polymerase subunit rpo7RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase 30 kDa polypeptide
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Core Vaccinia DNA-dependent RNA polymerase complex

SupramoleculeName: Core Vaccinia DNA-dependent RNA polymerase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Molecular weightExperimental: 500 KDa

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Supramolecule #2: DNA-dependent RNA polymerase subunits

SupramoleculeName: DNA-dependent RNA polymerase subunits / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#9
Source (natural)Organism: Vaccinia virus GLV-1h68

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Macromolecule #1: DNA-dependent RNA polymerase subunit rpo147

MacromoleculeName: DNA-dependent RNA polymerase subunit rpo147 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 146.995703 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MAVISKVTYS LYDQKEINAT DIIISHVKND DDIGTVKDGR LGAMDGALCK TCGKTELECF GHWGKVSIYK THIVKPEFIS EIIRLLNHI CIHCGLLRSR EPYSDDINLK ELSGHALRRL KDKILSKKKS CWNSECMQPY QKITFSKKKV CFVNKLDDIN V PNSLIYQK ...String:
MAVISKVTYS LYDQKEINAT DIIISHVKND DDIGTVKDGR LGAMDGALCK TCGKTELECF GHWGKVSIYK THIVKPEFIS EIIRLLNHI CIHCGLLRSR EPYSDDINLK ELSGHALRRL KDKILSKKKS CWNSECMQPY QKITFSKKKV CFVNKLDDIN V PNSLIYQK LISIHEKFWP LLEIHQYPAN LFYTDYFPIP PLIIRPAISF WIDSIPKETN ELTYLLGMIV KNCNLNADEQ VI QKAVIEY DDIKIISNNT TSINLSYITS GKNNMIRSYI VARRKDQTAR SVIGPSTSIT VNEVGMPAYI RNTLTEKIFV NAF TVDKVK QLLASNQVKF YFNKRLNQLT RIRQGKFIKN KIHLLPGDWV EVAVQEYTSI IFGRQPSLHR YNVIASSIRA TEGD TIKIS PGIANSQNAD FDGDEEWMIL EQNPKAVIEQ SILMYPTTLL KHDIHGAPVY GSIQDEIVAA YSLFRIQDLC LDEVL NILG KYGREFDPKG KCKFSGKDIY TYLIGEKINY PGLLKDGEII ANDVDSNFVV AMRHLSLAGL LSDHKSNVEG INFIIK SSY VFKRYLSIYG FGVTFKDLRP NSTFTNKLEA INVEKIELIK EAYAKYLNDV RDGKIVPLSK ALEADYVESM LSNLTNL NI REIEEHMRQT LIDDPDNNLL KMAKAGYKVN PTELMYILGT YGQQRIDGEP AETRVLGRVL PYYLPDSKDP EGRGYILN S LTKGLTGSQY YFSMLVARSQ STDIVCETSR TGTLARKIIK KMEDMVVDGY GQVVIGNTLI KYAANYTKIL GSVCKPVDL IYPDESMTWY LEISALWNKI KQGFVYSQKQ KLAKKTLAPF NFLVFVKPTT EDNAIKVKDL YDMIHNVIDD VREKYFFTVS NIDFMEYIF LTHLNPSRIR ITKETAITIF EKFYEKLNYT LGGGTPIGII SAQVLSEKFT QQALSSFHTT EKSGAVKQKL G FNEFNNLT NLSKNKTEII TLVSDDISKL QSVKINFEFV CLGELNPNIT LRKETDKYVV DIIVNRLYIK RAEITELVVE YM IERFISF SVIVKEWGME TFIEDEDNIR FTVYLNFVEP EELNLSKFMM VLPGAANKGK ISKFKIPISD YTGYDDFNQT KKL NKMTVE LMNLKELGSF DLENVNVYPG VWNTYDIFGI EAAREYLCEA MLNTYGEGFD YLYQPCDLLA SLLCASYEPE SVNK FKFGA ASTLKRATFG DNKALLNAAL HKKSEPINDN SSCHFFSKVP NIGTGYYKYF IDLGLLMRME RKLSDKISSQ KIKEM EETE DF

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Macromolecule #2: DNA-dependent RNA polymerase subunit rpo132

MacromoleculeName: DNA-dependent RNA polymerase subunit rpo132 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 133.526859 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MKKNTNSEMD QRLGYKFLVP DPKAGVFYRP LHFQYVSYSN FILHRLHEIL TVKRPLLSFK NNTERIMIEI SNVKVTPPDY SPIIASIKG KSYDALATFT VNIFKEVMTK EGISITKISS YEGKDSHLIK IPLLIGYGNK NPLDTAKYLV PNVIGGVFIN K QSVEKVGI ...String:
MKKNTNSEMD QRLGYKFLVP DPKAGVFYRP LHFQYVSYSN FILHRLHEIL TVKRPLLSFK NNTERIMIEI SNVKVTPPDY SPIIASIKG KSYDALATFT VNIFKEVMTK EGISITKISS YEGKDSHLIK IPLLIGYGNK NPLDTAKYLV PNVIGGVFIN K QSVEKVGI NLVEKITTWP KFRVVKPNSF TFSFSSVSPP NVLPTRYRHY KISLDISQLE ALNISSTKTF ITVNIVLLSQ YL SRVSLEF IRRSLSYDMP PEVVYLVNAI IDSAKRITES ITDFNIDTYI NDLVEAEHIK QKSQLTINEF KYEMLHNFLP HMN YTPDQL KGFYMISLLR KFLYCIFHTS RYPDRDSMVC HRILTYGKYF ETLAHDELEN YIGNIRNDIM NNHKNRGTYA VNIH VLTTP GLNHAFSSLL SGKFKKSDGS YRTHPHYSWM QNISIPRSVG FYPDQVKISK MFSVRKYHPS QYLYFCSSDV PERGP QVGL VSQLSVLSSI TNILTSEYLD LEKKICEYIR SYYKDDISYF ETGFPITIEN ALVASLNPNM ICDFVTDFRR RKRMGF FGN LEVGITLVRD HMNEIRINIG AGRLVRPFLV VDNGELMMDV CPELESRLDD MTFSDIQKEF PHVIEMVDIE QFTFSNV CE SVQKFRMMSK DERKQYDLCD FPAEFRDGYV ASSLVGINHN SGPRAILGCA QAKQAISCLS SDIRNKIDNG IHLMYPER P IVISKALETS KIAANCFGQH VTIALMSYKG INQEDGIIIK KQFIQRGGLD IVTAKKHQVE IPLENFNNKE RDRSNAYSK LESNGLVRLN AFLESGDAMA RNISSRTLED DFARDNQISF DVSEKYTDMY KSRVERVQVE LTDKVKVRVL TMKERRPILG DKFTTRTSQ KGTVAYVADE TELPYDENGI TPDVIINSTS IFSRKTISML IEVILTAAYS AKPYNNKGEN RPVCFPSSNE T SIDTYMQF AKQCYEHSNP KLSDEELSDK IFCEKILYDP ETDKPYASKV FFGPIYYLRL RHLTQDKATV RCRGKKTKLI RQ ANEGRKR GGGIKFGEME RDCLIAHGAA NTITEVLKDS EEDYQDVYVC ENCGDIAAQI KGINTCLRCS KLNLSPLLTK IDT THVSKV FLTQMNARGV KVKLDFERRP PSFYKPLDKV DLKPSFLV

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Macromolecule #3: DNA-directed RNA polymerase 35 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 35 kDa subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 35.430676 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MQHPREENSI VVELEPSLAT FIKQGFNNLV KWPLLNIGIV LSNTSTAVNE EWLTAVEHIP TMKIFYKHIH KILTREMGFL VYLKRSQSE RDNYITLYDF DYYIIDKDTN SVTMVDKPTE LKETLLHVFQ EYRLKSSQTI ELIAFSSGTV INEDIVSKLT F LDVEVFNR ...String:
MQHPREENSI VVELEPSLAT FIKQGFNNLV KWPLLNIGIV LSNTSTAVNE EWLTAVEHIP TMKIFYKHIH KILTREMGFL VYLKRSQSE RDNYITLYDF DYYIIDKDTN SVTMVDKPTE LKETLLHVFQ EYRLKSSQTI ELIAFSSGTV INEDIVSKLT F LDVEVFNR EYNNVKTIID PDFVFRSPFI VISPMGKLTF FVEVYSWFDF KSCFKDIIDF LEGALIANIH NHMIKVGNCD ET VSSYNPE SGMLFVNDLM TMNIVNFFGC NSRLESYHRF DMTKVDVELF IKALSDACKK ILSASNRL

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Macromolecule #4: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 21.36574 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString:
MNQYNVKYLA KILCLKTEIA RDPYAVINRN VLLRYTTDIE YNDLVTLITV RHKIDSMKTV FQVFNESSIN YTPVDDDYGE PIIITSYLQ KGHNKFPVNF LYIDVVISDL FPSFVRLDTT ETNIVNSVLQ TGDGKKTLRL PKMLETEIVV KILYRPNIPL K IVRFFRNN MVTGVEIADR SVISVAD

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Macromolecule #5: DNA-directed RNA polymerase 19 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 19 kDa subunit / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 19.020088 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString:
MADTDDIIDY ESDDLTEYED DEEEEEDGES LETSDIDPKS SYKIVESAST HIEDAHSNLK HIGNHISALK RRYTRRISLF EIAGIIAES YNLLQRGRLP LVSEFSDETM KQNMLHVIIQ EIEEGSCPIV IEKNGELLSV NDFDKDGLKF HLDYIIKIWK L QKRY

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Macromolecule #6: DNA-dependent RNA polymerase subunit rpo18

MacromoleculeName: DNA-dependent RNA polymerase subunit rpo18 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 17.917195 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString:
MSSFVTNGYL SVTLEPHELT LDIKTNIRNA VYKTYLHREI SGKMAKKIEI REDVELPLGE IVNNSVVINV PCVITYAYYH VGDIVRGTL NIEDESNVTI QCGDLICKLS RDSGTVSFSD SKYCFFRNGN AYDNGSEVTA VLMEAQQGIE SSFVFLANIV D S

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Macromolecule #7: RAP94 transcription factor

MacromoleculeName: RAP94 transcription factor / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 93.667633 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MDSKETILIE IIPKIKAYLL DANISPKSYD DFISRNKNIF VINLYNVSTI TEEDIRLLYT TIEQNIDADD QTLVAIFSYI GYKFEQAVK EEISTSLSFN DKNTTDEMTY NLYDLFFNTL DMYLRQKKIS ILVNDDVRGD VIVSYKNSDL VSSFNAELEP E IKKIPFNM ...String:
MDSKETILIE IIPKIKAYLL DANISPKSYD DFISRNKNIF VINLYNVSTI TEEDIRLLYT TIEQNIDADD QTLVAIFSYI GYKFEQAVK EEISTSLSFN DKNTTDEMTY NLYDLFFNTL DMYLRQKKIS ILVNDDVRGD VIVSYKNSDL VSSFNAELEP E IKKIPFNM KNLLPYLEKN LDQLRFSKKY LDFAYLCRHI GIPISKKKYN VRYVFLYKID GLSIPIIIKD FLDVKYVYLE NT GKIYKNS FSEDHNNSLS DWGKVIIPLL KDRHLYSYIF LSSYHLHSYY TDLIARDEPV FVKRKKLDII EIDEPEAWKR DVR VEFAPC EHQIRLKEAM KVDANYFTKI NNFANEFIYY EDGVAYCRVC GINIPIFNLD AADVIKNTVI VSTFNKTIFL SEPY SYFVH SQRFIFNIIM SFDNIMKSQT WVMKYNINRL ILNFLIDINS RRQEYEKKFS SEIKRGLFFL RLSANLFESQ VSSTE LFYV SKMLNLNYIV ALVIILNSSA DFIVSYMTSK NKTVEESTLK YAISVVIYDF LVKTRICEKG SLDTIVLFTD VYTSIM PEE LDLHFQRITL ELRKLVSIQR SALEPNYDVE SRGEELPLSA LKFFDTSTII VKTMAPVHTC VEQKIVAPTP SVEPTDA SL KNFKELTCDE DIKILIRVHD TNATKLVIFP SHLKIEIERK KLIIPLKSLY ITNTLKYYYS NSYLYVFRFG DPMPFEEE L IDHEHVQYKI NCYNILRYHL LPDSDVFVYF SNSLNREALE YAFYIFLSKY VNVKQWIDEN ITRIKELYMI NFNN

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Macromolecule #8: DNA-dependent RNA polymerase subunit rpo7

MacromoleculeName: DNA-dependent RNA polymerase subunit rpo7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 7.299715 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString:
MVFQLVCSTC GKDISHERYK LIIRKKSLKD VLVSVKNECC RLKLSTQIEP QRNLTVQPLL DIN

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Macromolecule #9: DNA-directed RNA polymerase 30 kDa polypeptide

MacromoleculeName: DNA-directed RNA polymerase 30 kDa polypeptide / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 29.834359 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MENVYISSYS SNEQTSMAVA ATDIRELLSQ YVDDANLEDL IEWAMEKSSK YYIKNIGNTK SNIEETKFES KNNIGIEYSK DSRNKLSYR NKPSIATNLE YKTLCDMIKG TSGTEKEFLR YLLFGIKCIK KGVEYNIDKI KDVSYNDYFN VLDEKYNTPC P NCKSRNTT ...String:
MENVYISSYS SNEQTSMAVA ATDIRELLSQ YVDDANLEDL IEWAMEKSSK YYIKNIGNTK SNIEETKFES KNNIGIEYSK DSRNKLSYR NKPSIATNLE YKTLCDMIKG TSGTEKEFLR YLLFGIKCIK KGVEYNIDKI KDVSYNDYFN VLDEKYNTPC P NCKSRNTT PMMIQTRAAD EPPLVRHACR DCKQHFKPPK FRAFRNLNVT TQSIHENKEI TEILPDNNPS PPESPEPASP ID DGLIRAT FDRNDEPPED DE

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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: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.5
GridModel: UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3609 / Average electron dose: 1.41 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 479618
CTF correctionSoftware: (Name: RELION (ver. 3.0), Warp)
Startup modelType of model: EMDB MAP
EMDB ID:

3218

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 152591
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6ric:
Structure of the core Vaccinia Virus DNA-dependent RNA polymerase complex

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