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- EMDB-17334: Cryo EM map of the vaccinia RNA polymerase intermediate pre-initi... -

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Basic information

Entry
Database: EMDB / ID: EMD-17334
TitleCryo EM map of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target)
Map data
Sample
  • Complex: Vaccinia DNA-directed RNA polymerase open promoter intermediate pre-initiation complex
    • Complex: Vaccinia DNA-directed RNA polymerase open promoter intermediate pre-initiation complex
      • Protein or peptide: x 12 types
    • Complex: Non-template DNA oligomer and Template DNA oligomer
      • DNA: x 2 types
  • Ligand: x 3 types
KeywordsRNA polymerase / RNAP / Vaccinia / MPox / PIC / pre-initiation complex / 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 / virion component / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / 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 / host cell cytoplasm / DNA-templated transcription / GTP binding / DNA binding / RNA binding / zinc ion binding / metal ion binding
Similarity search - Function
VITF-3 subunit protein / Poxvirus intermediate transcription factor / VITF-3 subunit protein / Poxvirus intermediate transcription factor / 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 ...VITF-3 subunit protein / Poxvirus intermediate transcription factor / VITF-3 subunit protein / Poxvirus intermediate transcription factor / 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 / Poxvirus mRNA capping enzyme, small subunit superfamily / Poxvirus mRNA capping enzyme, small subunit / mRNA capping enzyme, large subunit, ATPase/guanylyltransferase, virus / mRNA capping enzyme catalytic subunit, RNA triphosphatase domain / 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, 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 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 147 kDa polypeptide / mRNA-capping enzyme catalytic subunit / mRNA-capping enzyme regulatory subunit OPG124 / Intermediate transcription factor 3 small subunit / Intermediate transcription factor 3 large subunit / 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 / DNA-directed RNA polymerase 22 kDa subunit ...DNA-directed RNA polymerase 147 kDa polypeptide / mRNA-capping enzyme catalytic subunit / mRNA-capping enzyme regulatory subunit OPG124 / Intermediate transcription factor 3 small subunit / Intermediate transcription factor 3 large subunit / 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 / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsGrimm C / Jungwirth S / Fischer U
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target)
Authors: Grimm C / Jungwirth S / Fischer U
History
DepositionMay 10, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17334.png

Downloads & links

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Map

FileDownload / File: emd_17334.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 384 pix.
= 408.384 Å		1.06 Å/pix.
x 384 pix.
= 408.384 Å		1.06 Å/pix.
x 384 pix.
= 408.384 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.733
Minimum - Maximum-1.7076191 - 4.2954044
Average (Standard dev.)0.000121599034 (±0.11027713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 408.38403 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17334_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17334_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Vaccinia DNA-directed RNA polymerase open promoter intermediate p...

EntireName: Vaccinia DNA-directed RNA polymerase open promoter intermediate pre-initiation complex
Components
  • Complex: Vaccinia DNA-directed RNA polymerase open promoter intermediate pre-initiation complex
    • Complex: Vaccinia DNA-directed RNA polymerase open promoter intermediate pre-initiation 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 19 kDa subunit
      • Protein or peptide: DNA-directed RNA polymerase 18 kDa subunit
      • Protein or peptide: Intermediate transcription factor 3 large subunit
      • Protein or peptide: DNA-directed RNA polymerase 7 kDa subunit
      • Protein or peptide: mRNA-capping enzyme regulatory subunit OPG124
      • Protein or peptide: mRNA-capping enzyme catalytic subunit
      • Protein or peptide: DNA-directed RNA polymerase 30 kDa polypeptide
      • Protein or peptide: Intermediate transcription factor 3 small subunit
    • Complex: Non-template DNA oligomer and Template DNA oligomer
      • DNA: Non-template DNA oligomer
      • DNA: Template DNA oligomer
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Vaccinia DNA-directed RNA polymerase open promoter intermediate p...

SupramoleculeName: Vaccinia DNA-directed RNA polymerase open promoter intermediate pre-initiation complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Molecular weightTheoretical: 750 KDa

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Supramolecule #2: Vaccinia DNA-directed RNA polymerase open promoter intermediate p...

SupramoleculeName: Vaccinia DNA-directed RNA polymerase open promoter intermediate pre-initiation complex
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#9, #11-#12, #14
Source (natural)Organism: Vaccinia virus

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Supramolecule #3: Non-template DNA oligomer and Template DNA oligomer

SupramoleculeName: Non-template DNA oligomer and Template DNA oligomer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #10, #13
Source (natural)Organism: Vaccinia virus

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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
Details: MNQYNVKYLAKILCLKTEIARDPYAVINRNVLLRYTTDIEYNDLVTLITVRHKIDSMKTVFQVFNESSIN YTPVDDDYGEPIIITSYLQKGHNKFPVNFLYIDVVISDLFPSFVRLDTTETNIVNSVLQTGDGKKTLRLP KMLETEIVVKILYRPNIPLKIVRFFRNNMVTGVEIADRSVISVAD
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 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

UniProtKB: DNA-directed RNA polymerase 19 kDa subunit

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Macromolecule #6: DNA-directed RNA polymerase 18 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 18 kDa subunit / 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

UniProtKB: DNA-directed RNA polymerase 18 kDa subunit

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Macromolecule #7: Intermediate transcription factor 3 large subunit

MacromoleculeName: Intermediate transcription factor 3 large subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 44.66243 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MDNLFTFLHE IEDRYARTIF NFHLISCDEI GDIYGLMKER ISSEDMFDNI VYNKDIHPAI KKLVYCDIQL TKHIINQNTY PVFNDSSQV KCCHYFDINS DNSNISSRTV EIFEREKSSL VSYIKTTNKK RKVNYGEIKK TVHGGTNANY FSGKKSDEYL S TTVRSNIN ...String:
MDNLFTFLHE IEDRYARTIF NFHLISCDEI GDIYGLMKER ISSEDMFDNI VYNKDIHPAI KKLVYCDIQL TKHIINQNTY PVFNDSSQV KCCHYFDINS DNSNISSRTV EIFEREKSSL VSYIKTTNKK RKVNYGEIKK TVHGGTNANY FSGKKSDEYL S TTVRSNIN QPWIKTISKR MRVDIINHSI VTRGKSSILQ TIEIIFTNRT CVKIFKDSTM HIILSKDKDE KGCIHMIDKL FY VYYNLFL LFEDIIQNEY FKEVANVVNH VLTATALDEK LFLIKKMAEH DVYGVSNFKI GMFNLTFIKS LDHTVFPSLL DED SKIKFF KGKKLNIVAL RSLEDCINYV TKSENMIEMM KERSTILNSI DIETESVDRL KELLLK

UniProtKB: Intermediate transcription factor 3 large subunit

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Macromolecule #8: DNA-directed RNA polymerase 7 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 7 kDa subunit / type: protein_or_peptide / ID: 8 / 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 #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 #11: mRNA-capping enzyme catalytic subunit

MacromoleculeName: mRNA-capping enzyme catalytic subunit / type: protein_or_peptide / ID: 11 / 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 #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

UniProtKB: DNA-directed RNA polymerase 30 kDa polypeptide

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Macromolecule #14: Intermediate transcription factor 3 small subunit

MacromoleculeName: Intermediate transcription factor 3 small subunit / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 33.618648 KDa
Recombinant expressionOrganism: Vaccinia virus
SequenceString: MFEPVPDLNL EASVELGEVN IDQTTPMIKE NSGFISRSRR LFAHRSKDDE RKLALRFFLQ RLYFLDHREI HYLFRCVDAV KDVTITKKN NIIVAPYIAL LTIASKGCKL TETMIEAFFP ELYNEHSKKF KFNSQVSIIQ EKLGYQFGNY HVYDFEPYYS T VALAIRDE ...String:
MFEPVPDLNL EASVELGEVN IDQTTPMIKE NSGFISRSRR LFAHRSKDDE RKLALRFFLQ RLYFLDHREI HYLFRCVDAV KDVTITKKN NIIVAPYIAL LTIASKGCKL TETMIEAFFP ELYNEHSKKF KFNSQVSIIQ EKLGYQFGNY HVYDFEPYYS T VALAIRDE HSSGIFNIRQ ESYLVSSLSE ITYRFYLINL KSDLVQWSAS TGAVINQMVN TVLITVYEKL QLVIENDSQF TC SLAVESK LPIKLLKDRN ELFTKFINEL KKTSSFKISK RDKDTLLKYF T

UniProtKB: Intermediate transcription factor 3 small subunit

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Macromolecule #10: Non-template DNA oligomer

MacromoleculeName: Non-template DNA oligomer / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 21.587969 KDa
SequenceString: (DG)(DC)(DA)(DG)(DC)(DC)(DA)(DT)(DT)(DT) (DA)(DA)(DC)(DT)(DT)(DT)(DA)(DA)(DA)(DT) (DA)(DA)(DT)(DT)(DT)(DA)(DC)(DA)(DA) (DA)(DA)(DA)(DT)(DT)(DT)(DA)(DA)(DA)(DA) (DT) (DG)(DA)(DG)(DC)(DA)(DT) ...String:
(DG)(DC)(DA)(DG)(DC)(DC)(DA)(DT)(DT)(DT) (DA)(DA)(DC)(DT)(DT)(DT)(DA)(DA)(DA)(DT) (DA)(DA)(DT)(DT)(DT)(DA)(DC)(DA)(DA) (DA)(DA)(DA)(DT)(DT)(DT)(DA)(DA)(DA)(DA) (DT) (DG)(DA)(DG)(DC)(DA)(DT)(DC)(DC) (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DA)(DT) (DC)(DC) (DA)(DT)(DA)(DA)(DA)(DG)(DG) (DG)(DG)(DG)

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Macromolecule #13: Template DNA oligomer

MacromoleculeName: Template DNA oligomer / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 21.675945 KDa
SequenceString: (DC)(DC)(DC)(DC)(DC)(DT)(DT)(DT)(DA)(DT) (DG)(DG)(DA)(DT)(DT)(DT)(DT)(DT)(DA)(DT) (DA)(DG)(DG)(DG)(DA)(DT)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DA)(DA)(DT)(DA)(DT)(DA) (DA) (DT)(DT)(DT)(DG)(DT)(DA) ...String:
(DC)(DC)(DC)(DC)(DC)(DT)(DT)(DT)(DA)(DT) (DG)(DG)(DA)(DT)(DT)(DT)(DT)(DT)(DA)(DT) (DA)(DG)(DG)(DG)(DA)(DT)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DA)(DA)(DT)(DA)(DT)(DA) (DA) (DT)(DT)(DT)(DG)(DT)(DA)(DA)(DA) (DT)(DT)(DA)(DT)(DT)(DT)(DA)(DA)(DA)(DG) (DT)(DT) (DA)(DA)(DA)(DT)(DG)(DG)(DC) (DT)(DG)(DC)

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Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #17: water

MacromoleculeName: water / type: ligand / ID: 17 / Number of copies: 508 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
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: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9318600
Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 1421158
FSC plot (resolution estimation)

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