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- EMDB-19442: Structure of the complete Vaccinia DNA-dependent RNA polymerase c... -

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Basic information

Entry
Database: EMDB / ID: EMD-19442
TitleStructure of the complete Vaccinia DNA-dependent RNA polymerase complex at 2.65A resolution
Map data
Sample
  • Complex: complete Vaccinia DNA-dependent RNA polymerase complex
    • Protein or peptide: x 14 types
    • RNA: x 1 types
  • Ligand: x 3 types
KeywordsVACCINIA / RNA POLYMERASE / RNA POLYMERASE COMPLEX / RNAP / VRNAP / COMPLETE VRNAP / VIRAL PROTEIN / TRANSCRIPTION
Function / homology
Function and homology information


inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / viral transcription / DNA-directed RNA polymerase complex / ribonucleoside triphosphate phosphatase activity / DNA-templated transcription termination / ribonucleoside binding / virion component ...inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / viral transcription / DNA-directed RNA polymerase complex / ribonucleoside triphosphate phosphatase activity / DNA-templated transcription termination / ribonucleoside binding / virion component / : / : / : / : / : / : / DNA-directed RNA polymerase / mRNA guanylyltransferase activity / nucleoside-triphosphate phosphatase / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / DNA-binding transcription factor activity / DNA-templated transcription / GTP binding / positive regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding
Similarity search - Function
Poxvirus early transcription factor, large subunit / Virion core protein, vaccinia E11L type / Nucleoside triphosphatase I, C-terminal / Poxvirus early transcription factor (VETF), large subunit / Chordopoxvirus E11 protein / Nucleoside triphosphatase I C-terminal / 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 / : ...Poxvirus early transcription factor, large subunit / Virion core protein, vaccinia E11L type / Nucleoside triphosphatase I, C-terminal / Poxvirus early transcription factor (VETF), large subunit / Chordopoxvirus E11 protein / Nucleoside triphosphatase I C-terminal / 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 / Poxvirus mRNA capping enzyme, small subunit / mRNA capping enzyme, large subunit, ATPase/guanylyltransferase, virus / Poxvirus mRNA capping enzyme, small subunit superfamily / Poxvirus mRNA capping enzyme, small subunit / mRNA capping enzyme catalytic subunit, RNA triphosphatase domain / 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 / mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56) domain profile. / SNF2, N-terminal / SNF2-related domain / 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 / DNA-directed RNA polymerase, subunit beta-prime / RPB6/omega subunit-like superfamily / Helicase conserved C-terminal domain / RNA polymerase Rpb1, clamp domain superfamily / 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 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA-directed RNA polymerase 147 kDa polypeptide / Early transcription factor 82 kDa subunit / Nucleoside triphosphatase I / mRNA-capping enzyme catalytic subunit / mRNA-capping enzyme regulatory subunit OPG124 / DNA-directed RNA polymerase 18 kDa subunit / DNA-directed RNA polymerase 30 kDa polypeptide / DNA-directed RNA polymerase 35 kDa subunit / DNA-directed RNA polymerase 7 kDa subunit / RNA polymerase-associated transcription-specificity factor RAP94 ...DNA-directed RNA polymerase 147 kDa polypeptide / Early transcription factor 82 kDa subunit / Nucleoside triphosphatase I / mRNA-capping enzyme catalytic subunit / mRNA-capping enzyme regulatory subunit OPG124 / DNA-directed RNA polymerase 18 kDa subunit / DNA-directed RNA polymerase 30 kDa polypeptide / DNA-directed RNA polymerase 35 kDa subunit / DNA-directed RNA polymerase 7 kDa subunit / RNA polymerase-associated transcription-specificity factor RAP94 / Core protein OPG073 / DNA-directed RNA polymerase 22 kDa subunit / DNA-directed RNA polymerase 19 kDa subunit / DNA-directed RNA polymerase 133 kDa polypeptide
Similarity search - Component
Biological speciesVaccinia virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsGrimm C / Bartuli J / Fischer U
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Structure of the complete Vaccinia DNA-dependent RNA polymerase complex at 2.65A resolution
Authors: Grimm C / Bartuli J / Fischer U
History
DepositionJan 18, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19442.png

Downloads & links

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Map

FileDownload / File: emd_19442.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 382.86 Å		1.06 Å/pix.
x 360 pix.
= 382.86 Å		1.06 Å/pix.
x 360 pix.
= 382.86 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.33752817 - 1.649696
Average (Standard dev.)-0.0034866373 (±0.07004725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 382.86002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19442_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_19442_half_map_2.map
Projections & Slices
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Sample components

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Entire : complete Vaccinia DNA-dependent RNA polymerase complex

EntireName: complete Vaccinia DNA-dependent RNA polymerase complex
Components
  • Complex: complete Vaccinia DNA-dependent RNA polymerase complex
    • Protein or peptide: DNA-directed RNA polymerase 147 kDa polypeptide
    • Protein or peptide: DNA-directed RNA polymerase 133 kDa polypeptide
    • Protein or peptide: DNA-directed RNA polymerase 35 kDa subunit
    • Protein or peptide: DNA-directed RNA polymerase 22 kDa subunit
    • Protein or peptide: DNA-directed RNA polymerase 18 kDa subunit
    • Protein or peptide: RNA polymerase-associated transcription-specificity factor RAP94
    • Protein or peptide: DNA-directed RNA polymerase 7 kDa subunit
    • Protein or peptide: Early transcription factor 82 kDa subunit
    • Protein or peptide: mRNA-capping enzyme regulatory subunit OPG124
    • Protein or peptide: mRNA-capping enzyme catalytic subunit
    • Protein or peptide: Core protein OPG073
    • Protein or peptide: DNA-directed RNA polymerase 30 kDa polypeptide
    • RNA: URQ-UUG1-1 tRNA (72-MER)
    • Protein or peptide: Nucleoside triphosphatase I
    • Protein or peptide: DNA-directed RNA polymerase 19 kDa subunit
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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

SupramoleculeName: complete Vaccinia DNA-dependent RNA polymerase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 870 KDa

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Macromolecule #1: DNA-directed RNA polymerase 147 kDa polypeptide

MacromoleculeName: DNA-directed RNA polymerase 147 kDa polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
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

UniProtKB: DNA-directed RNA polymerase 147 kDa polypeptide

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Macromolecule #2: DNA-directed RNA polymerase 133 kDa polypeptide

MacromoleculeName: DNA-directed RNA polymerase 133 kDa polypeptide / 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

UniProtKB: DNA-directed RNA polymerase 133 kDa polypeptide

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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
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

UniProtKB: DNA-directed RNA polymerase 35 kDa subunit

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Macromolecule #4: DNA-directed RNA polymerase 22 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 22 kDa 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

UniProtKB: DNA-directed RNA polymerase 22 kDa subunit

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Macromolecule #5: DNA-directed RNA polymerase 18 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 18 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: 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

UniProtKB: DNA-directed RNA polymerase 18 kDa subunit

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Macromolecule #6: RNA polymerase-associated transcription-specificity factor RAP94

MacromoleculeName: RNA polymerase-associated transcription-specificity factor RAP94
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus
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

UniProtKB: RNA polymerase-associated transcription-specificity factor RAP94

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Macromolecule #7: DNA-directed RNA polymerase 7 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 7 kDa subunit / 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

UniProtKB: DNA-directed RNA polymerase 7 kDa subunit

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Macromolecule #8: Early transcription factor 82 kDa subunit

MacromoleculeName: Early transcription factor 82 kDa subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 82.398906 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MRYIVSPQLV LQVGKGQEVE RALYLTPYDY IDEKSPIYYF LRSHLNIQQP EIVKRHILLT LRMTQLKGYL GNLLDIKDDI IIYSHKNNL EYSYVDNTIF NPFVYTQKKT LLKNDSFLYN VYPGACDFLV IWVARACDTS IPEFGSYEDV DNNIIKFETM L MEVFPQLD ...String:
MRYIVSPQLV LQVGKGQEVE RALYLTPYDY IDEKSPIYYF LRSHLNIQQP EIVKRHILLT LRMTQLKGYL GNLLDIKDDI IIYSHKNNL EYSYVDNTIF NPFVYTQKKT LLKNDSFLYN VYPGACDFLV IWVARACDTS IPEFGSYEDV DNNIIKFETM L MEVFPQLD LDITVESKFN NIFRTNLKLT GLKKIIQRVQ DLDINYKSLL SRYDEHFINM TGNHFILNDE QLNLSIWDLD GT LALSSDG DTVMINNVKL FTDLVSDIDT QMERIKGDIT YKVHLATPIN SRIKLDIETS FIFIETATNN ILLSSDKKIS IIL AKNHIS IKVKNHIPNI EKYFTFLVIA INAMFNSVQK SADFTKVETV YWSRICQNTK NKNRKPIIIN YLDPGMKKIS NNFY RSDEK EVFINDNGIM FTCMDPLGKY NKVGFLNIFH DMRKYCIPCC FLHDQSHRST FSSCVHQIDV EKKIVSPYIL NFGKV VTES KMSFLPIIFD AFLNDGMTAN MEQDNKRLKE TSGYHIVRCC AGDDIVRLRT TSDIIQFVNE DKNILIVNDM VYFPMN ASD IGKKIHILIQ EIVHEVMIVK KKESSDKIDF FPPNYKLLKD LFPKQTIQTP IQSDAGMVLT TDGFYIDGKL FNEDLSS KY VTFTKNVIAS DAVAKYFSPL FKYVISEAKD RFIKTWMINI MIHMNVDPNN IIPTLEKYYP NSGRAQIN

UniProtKB: Early transcription factor 82 kDa subunit

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Macromolecule #9: mRNA-capping enzyme regulatory subunit OPG124

MacromoleculeName: mRNA-capping enzyme regulatory subunit OPG124 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
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

UniProtKB: mRNA-capping enzyme regulatory subunit OPG124

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Macromolecule #10: mRNA-capping enzyme catalytic subunit

MacromoleculeName: mRNA-capping enzyme catalytic subunit / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: mRNA 5'-phosphatase
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

UniProtKB: mRNA-capping enzyme catalytic subunit

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Macromolecule #11: Core protein OPG073

MacromoleculeName: Core protein OPG073 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 14.91409 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString:
MELVNIFLET DAGRVKFAIK NTDDVCASEL INKFVELLSE YIHIDQSEFY LVVKDKDIFY FKCDRGSISI VNNEFYVFDE PLLFVKDFT NVTGVEFIVT ETMPCRIIPK NNHAVISVVT NHKFYNGLSL

UniProtKB: Core protein OPG073

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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: 30.074293 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 TEILPDNNP(SEP) PPE(SEP) PEPA(SEP) PIDDGLIRAT FDRNDEPPED DE

UniProtKB: DNA-directed RNA polymerase 30 kDa polypeptide

+
Macromolecule #14: Nucleoside triphosphatase I

MacromoleculeName: Nucleoside triphosphatase I / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO / EC number: nucleoside-triphosphate phosphatase
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 72.46532 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MSKSHAAYID YALRRTTNMP VEMMGSDVVR LKDYQHFVAR VFLGLDSMHS LLLFHETGVG KTMTTVYILK HLKDIYTNWA IILLVKKAL IEDPWMNTIL RYAPEITKDC IFINYDDQNF RNKFFTNIKT INSKSRICVI IDECHNFISK SLIKEDGKIR P TRSVYNFL ...String:
MSKSHAAYID YALRRTTNMP VEMMGSDVVR LKDYQHFVAR VFLGLDSMHS LLLFHETGVG KTMTTVYILK HLKDIYTNWA IILLVKKAL IEDPWMNTIL RYAPEITKDC IFINYDDQNF RNKFFTNIKT INSKSRICVI IDECHNFISK SLIKEDGKIR P TRSVYNFL SKTIALKNHK MICLSATPIV NSVQEFTMLV NLLRPGSLQH QSLFENKRLV DEKELVSKLG GLCSYIVNNE FS IFDDVEG SASFAKKTVL MRYVNMSKKQ EEIYQKAKLA EIKTGISSFR ILRRMATTFT FDSFPERQNR DPGEYAQEIA TLY NDFKNS LRDREFSKSA LDTFKKGELL KGDASAADIS LFTELKEKSV KFIDVCLGIL ASHGKCLVFE PFVNQSGIEI LLLY FKVFG ISNIEFSSRT KDTRIKAVAE FNQESNTNGE CIKTCVFSSS GGEGISFFSI NDIFILDMTW NEASLRQIVG RAIRL NSHV LTPPERRYVN VHFIMARLSN GMPTVDEDLF EIIQSKSKEF VQLFRVFKHT SLEWIHANEK DFSPIDNESG WKTLVS RAI DLSSKKNITN KLIEGTNIWY SNSNRLMSIN RGFKGVDGRV YDVDGNYLHD MPDNPVIKIH DGKLIYIF

UniProtKB: Nucleoside triphosphatase I

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Macromolecule #15: DNA-directed RNA polymerase 19 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 19 kDa subunit / type: protein_or_peptide / ID: 15 / 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

UniProtKB: DNA-directed RNA polymerase 19 kDa subunit

+
Macromolecule #13: URQ-UUG1-1 tRNA (72-MER)

MacromoleculeName: URQ-UUG1-1 tRNA (72-MER) / type: rna / ID: 13 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.136703 KDa
SequenceString:
GGUCCCAUGG UGUAAUGGUU AGCACUCUGG A(OMC)UUUGAAUC CAGCGAUCCG AGUUCA(1MA)AUC UCGGUGGGAC CU

GENBANK: GENBANK: OY540809.1

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Macromolecule #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #18: water

MacromoleculeName: water / type: ligand / ID: 18 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 78.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 934606
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial modelPDB ID:

6rfl


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8rqk:
Structure of the complete Vaccinia DNA-dependent RNA polymerase complex at 2.65A resolution

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