[English] 日本語
Yorodumi
- EMDB-4890: Structure of Vaccinia Virus DNA-dependent RNA polymerase co-trans... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4890
TitleStructure of Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping complex
Map dataPost-processed cryo-EM map.
Sample
  • Complex: Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping complex
    • Complex: DNA-dependent RNA polymerase subunitRNA polymerase
      • Protein or peptide: x 10 types
    • Complex: RNA
      • RNA: x 1 types
    • Complex: synthetic
      • DNA: x 2 types
  • Ligand: x 3 types
Function / homology
Function and homology information


polynucleotide 5'-phosphatase / inorganic triphosphate phosphatase activity / DNA-templated viral transcription / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / virion component => GO:0044423 / viral transcription / DNA-directed RNA polymerase complex / virion component ...polynucleotide 5'-phosphatase / inorganic triphosphate phosphatase activity / DNA-templated viral transcription / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / virion component => GO:0044423 / viral transcription / DNA-directed RNA polymerase complex / virion component / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA-templated transcription / GTP binding / DNA binding / RNA binding / zinc ion binding / metal ion binding
Similarity search - Function
mRNA-capping enzyme catalytic subunit, OB fold domain superfamily / mRNA-capping enzyme catalytic subunit, nucleotidyltransferase domain superfamily / mRNA-capping enzyme catalytic subunit, RNA triphosphatase domain superfamily / : / : / mRNA capping enzyme catalytic subunit, GTase, NTPase domain / mRNA-capping enzyme catalytic subunit, GTase, OB fold / mRNA capping enzyme, large subunit, ATPase/guanylyltransferase, virus / mRNA capping enzyme catalytic subunit, RNA triphosphatase domain / Poxvirus mRNA capping enzyme, small subunit ...mRNA-capping enzyme catalytic subunit, OB fold domain superfamily / mRNA-capping enzyme catalytic subunit, nucleotidyltransferase domain superfamily / mRNA-capping enzyme catalytic subunit, RNA triphosphatase domain superfamily / : / : / mRNA capping enzyme catalytic subunit, GTase, NTPase domain / mRNA-capping enzyme catalytic subunit, GTase, OB fold / mRNA capping enzyme, large subunit, ATPase/guanylyltransferase, virus / mRNA capping enzyme catalytic subunit, RNA triphosphatase domain / Poxvirus mRNA capping enzyme, small subunit / Poxvirus mRNA capping enzyme, small subunit superfamily / Poxvirus mRNA capping enzyme, small subunit / 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 / mRNA (guanine-N(7))-methyltransferase domain / mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56) domain profile. / 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 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase 30 kDa polypeptide / DNA-directed RNA polymerase 7 kDa subunit / DNA-directed RNA polymerase subunit / GTP--RNA guanylyltransferase / DNA-directed RNA polymerase 18 kDa subunit / Virus termination factor small subunit / DNA-directed RNA polymerase 19 kDa subunit / DNA-directed RNA polymerase / DNA-directed RNA polymerase 35 kDa subunit / DNA-directed RNA polymerase 30 kDa polypeptide ...DNA-directed RNA polymerase 30 kDa polypeptide / DNA-directed RNA polymerase 7 kDa subunit / DNA-directed RNA polymerase subunit / GTP--RNA guanylyltransferase / DNA-directed RNA polymerase 18 kDa subunit / Virus termination factor small subunit / DNA-directed RNA polymerase 19 kDa subunit / DNA-directed RNA polymerase / DNA-directed RNA polymerase 35 kDa subunit / DNA-directed RNA polymerase 30 kDa polypeptide / DNA-directed RNA polymerase 147 kDa polypeptide / DNA-directed RNA polymerase 35 kDa subunit / mRNA-capping enzyme catalytic subunit / mRNA-capping enzyme regulatory subunit OPG124 / DNA-directed RNA polymerase 7 kDa subunit / DNA-directed RNA polymerase 22 kDa subunit / DNA-directed RNA polymerase 147 kDa polypeptide / DNA-directed RNA polymerase 133 kDa polypeptide / DNA-directed RNA polymerase 19 kDa subunit / DNA-directed RNA polymerase 18 kDa subunit
Similarity search - Component
Biological speciesVaccinia virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHillen HS / Bartuli J / Grimm C / Dienemann C / Bedenk K / Szalar A / Fischer U / Cramer P
Funding support Germany, 7 items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
German Federal Ministry for Education and ResearchEXC 2067/1- 390729940 Germany
German Research FoundationSPP1935 Germany
Volkswagen Foundation Germany
European Research CouncilTRANSREGULON Germany
German Research FoundationFi 573 18-1 Germany
German Research FoundationFi 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) releaseDec 18, 2019-
Map releaseDec 18, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6rie
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4890.png

Downloads & links

-
Map

FileDownload / File: emd_4890.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed cryo-EM map.
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.0769682 - 0.1522492
Average (Standard dev.)0.00023477204 (±0.0035679077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 356.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z357.000357.000357.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0770.1520.000

-
Supplemental data

-
Mask #1

Fileemd_4890_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Global 3D refinement map.

Fileemd_4890_additional_1.map
AnnotationGlobal 3D refinement map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Mask used in refinement.

Fileemd_4890_additional_2.map
AnnotationMask used in refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half-map 1.

Fileemd_4890_additional_3.map
AnnotationHalf-map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half-map 2.

Fileemd_4890_additional_4.map
AnnotationHalf-map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_4890_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_4890_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional ca...

EntireName: Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping complex
Components
  • Complex: Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping complex
    • Complex: DNA-dependent RNA polymerase subunitRNA 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: DNA-dependent RNA polymerase subunit rpo7RNA polymerase
      • Protein or peptide: Small subunit of mRNA capping enzyme
      • Protein or peptide: Large subunit of mRNA capping enzyme
      • Protein or peptide: DNA-directed RNA polymerase 30 kDa polypeptide
    • Complex: RNA
      • RNA: RNA
    • Complex: synthetic
      • DNA: Non-template DNA strand
      • DNA: Template strand DNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINES-Adenosyl methionine

+
Supramolecule #1: Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional ca...

SupramoleculeName: Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Molecular weightTheoretical: 580 KDa

+
Supramolecule #2: DNA-dependent RNA polymerase subunit

SupramoleculeName: DNA-dependent RNA polymerase subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#8, #10, #12
Source (natural)Organism: Vaccinia virus
Recombinant expressionOrganism: Vaccinia virus

+
Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11
Source (natural)Organism: Vaccinia virus
Recombinant expressionOrganism: Enterobacteria phage T7 (virus)

+
Supramolecule #4: synthetic

SupramoleculeName: synthetic / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #9, #13
Source (natural)Organism: Vaccinia virus
Recombinant expressionOrganism: synthetic construct (others)

+
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
Source (natural)Organism: Vaccinia virus
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

+
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
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

+
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
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

+
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
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

+
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
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

+
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
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

+
Macromolecule #7: DNA-dependent RNA polymerase subunit rpo7

MacromoleculeName: DNA-dependent RNA polymerase subunit rpo7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 7.299715 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString:
MVFQLVCSTC GKDISHERYK LIIRKKSLKD VLVSVKNECC RLKLSTQIEP QRNLTVQPLL DIN

+
Macromolecule #8: Small subunit of mRNA capping enzyme

MacromoleculeName: Small subunit of mRNA capping enzyme / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: mRNA (guanine-N7)-methyltransferase
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 33.396656 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MDEIVKNIRE GTHVLLPFYE TLPELNLSLG KSPLPSLEYG ANYFLQISRV NDLNRMPTDM LKLFTHDIML PESDLDKVYE ILKINSVKY YGRSTKADAV VADLSARNKL FKRERDAIKS NNHLTENNLY ISDYKMLTFD VFRPLFDFVN EKYCIIKLPT L FGRGVIDT ...String:
MDEIVKNIRE GTHVLLPFYE TLPELNLSLG KSPLPSLEYG ANYFLQISRV NDLNRMPTDM LKLFTHDIML PESDLDKVYE ILKINSVKY YGRSTKADAV VADLSARNKL FKRERDAIKS NNHLTENNLY ISDYKMLTFD VFRPLFDFVN EKYCIIKLPT L FGRGVIDT MRIYCSLFKN VRLLKCVSDS WLKDSAIMVA SDVCKKNLDL FMSHVKSVTK SSSWKDVNSV QFSILNNPVD TE FINKFLE FSNRVYEALY YVHSLLYSSM TSDSKSIENK HQRRLVKLLL

+
Macromolecule #10: Large subunit of mRNA capping enzyme

MacromoleculeName: Large subunit of mRNA capping enzyme / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 96.888758 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MDANVVSFST IATYIDALAK NASELEQRST AYEINNELEL VFIKPPLITL TNVVNISTIQ ESFIRFTVTN KEGVKIRTKI PLSKVHGLD VKNVQLVDAI DNIVWEKKSL VTENRLHKEC LLRLSTEERH IFLDYKKYGS SIRLELVNLI QAKTKNFTID F KLKYFLGS ...String:
MDANVVSFST IATYIDALAK NASELEQRST AYEINNELEL VFIKPPLITL TNVVNISTIQ ESFIRFTVTN KEGVKIRTKI PLSKVHGLD VKNVQLVDAI DNIVWEKKSL VTENRLHKEC LLRLSTEERH IFLDYKKYGS SIRLELVNLI QAKTKNFTID F KLKYFLGS GAQSKSSLLH AINHPKSRPN TSLEIEFTPR DNETVPYDEL IKELTTLSRH IFMASPENVI LSPPINAPIK TF MLPKQDI VGLDLENLYA VTKTDGIPIT IRVTSNGLYC YFTHLGYIIR YPVKRIIDSE VVVFGEAVKD KNWTVYLIKL IEP VNAIND RLEESKYVES KLVDICDRIV FKSKKYEGPF TTTSEVVDML STYLPKQPEG VILFYSKGPK SNIDFKIKKE NTID QTANV VFRYMSSEPI IFGESSIFVE YKKFSNDKGF PKEYGSGKIV LYNGVNYLNN IYCLEYINTH NEVGIKSVVV PIKFI AEFL VNGEILKPRI DKTMKYINSE DYYGNQHNII VEHLRDQSIK IGDIFNEDKL SDVGHQYANN DKFRLNPEVS YFTNKR TRG PLGILSNYVK TLLISMYCSK TFLDDSNKRK VLAIDFGNGA DLEKYFYGEI ALLVATDPDA DAIARGNERY NKLNSGI KT KYYKFDYIQE TIRSDTFVSS VREVFYFGKF NIIDWQFAIH YSFHPRHYAT VMNNLSELTA SGGKVLITTM DGDKLSKL T DKKTFIIHKN LPSSENYMSV EKIADDRIVV YNPSTMSTPM TEYIIKKNDI VRVFNEYGFV LVDNVDFATI IERSKKFIN GASTMEDRPS TKNFFELNRG AIKCEGLDVE DLLSYYVVYV FSKR

+
Macromolecule #12: DNA-directed RNA polymerase 30 kDa polypeptide

MacromoleculeName: DNA-directed RNA polymerase 30 kDa polypeptide / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus
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

+
Macromolecule #9: Non-template DNA strand

MacromoleculeName: Non-template DNA strand / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 14.775473 KDa
SequenceString:
(DG)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DG)(DG) (DC)(DA)(DT)(DC)(DC)(DC)(DA)(DT)(DG)(DC) (DG)(DT)(DT)(DG)(DA)(DG)(DG)(DA)(DC) (DT)(DC)(DT)(DT)(DA)(DT)(DC)(DC)(DG)(DA) (DT) (DC)(DA)(DT)(DA)(DA)(DG)(DT)(DC)

+
Macromolecule #13: Template strand DNA

MacromoleculeName: Template strand DNA / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 14.786517 KDa
SequenceString:
(DG)(DA)(DC)(DT)(DT)(DA)(DT)(DG)(DA)(DT) (DC)(DG)(DG)(DA)(DT)(DA)(DA)(DG)(DA)(DG) (DT)(DC)(DC)(DA)(DG)(DC)(DC)(DA)(DA) (DT)(DG)(DA)(DC)(DA)(DG)(DA)(DT)(DG)(DC) (DC) (DT)(DC)(DA)(DT)(DA)(DG)(DC)(DC)

+
Macromolecule #11: RNA

MacromoleculeName: RNA / type: rna / ID: 11 / Number of copies: 1
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 9.822829 KDa
SequenceString:
(GDP)AGUUGUAAU AACAAGGGAA AUGUCAUUGG

+
Macromolecule #14: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #16: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 16 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE / S-Adenosyl methionine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

-
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 / 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 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4958 / Average electron dose: 1.02 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 632458
CTF correctionSoftware: (Name: RELION (ver. 3.0), Warp)
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model generated by cryoSPARC.
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 77706
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4ckb

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6rie:
Structure of Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more