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- EMDB-16476: Cryo EM structure of the vaccinia complete RNA polymerase complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-16476
TitleCryo EM structure of the vaccinia complete RNA polymerase complex lacking the capping enzyme
Map dataCryo EM map of the complete vaccinia RNA polymerase lacking the capping enzyme
Sample
  • Complex: Vaccinia complete RNA polymerase complex lacking the capping enzyme
    • Protein or peptide: x 12 types
    • RNA: x 1 types
  • Ligand: x 3 types
KeywordsRNA polymerase / RNAP / DNA-dependent RNA polymerase / VIRAL PROTEIN
Function / homology
Function and homology information


DNA-templated viral transcription / ATP-dependent chromatin remodeler activity / viral transcription / ribonucleoside triphosphate phosphatase activity / DNA-directed RNA polymerase complex / virion component / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...DNA-templated viral transcription / ATP-dependent chromatin remodeler activity / viral transcription / ribonucleoside triphosphate phosphatase activity / DNA-directed RNA polymerase complex / virion component / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / nucleoside-triphosphate phosphatase / host cell cytoplasm / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / ATP binding / metal ion binding
Similarity search - Function
Virion core protein, vaccinia E11L type / Chordopoxvirus E11 protein / Poxvirus early transcription factor, large subunit / Nucleoside triphosphatase I, C-terminal / Poxvirus early transcription factor (VETF), large subunit / Nucleoside triphosphatase I C-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 ...Virion core protein, vaccinia E11L type / Chordopoxvirus E11 protein / Poxvirus early transcription factor, large subunit / Nucleoside triphosphatase I, C-terminal / Poxvirus early transcription factor (VETF), large subunit / Nucleoside triphosphatase I C-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 / 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 / Helicase conserved C-terminal domain / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA-directed RNA polymerase 18 kDa subunit / Nucleoside triphosphatase I / DNA-directed RNA polymerase 147 kDa polypeptide / Early transcription factor 82 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 18 kDa subunit / Nucleoside triphosphatase I / DNA-directed RNA polymerase 147 kDa polypeptide / Early transcription factor 82 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 GLV-1h68
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsGrimm G / Bartuli J / Fischer U
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Fi573/23-1 Germany
Volkswagen Foundation9B813 Germany
CitationJournal: Cell / Year: 2019
Title: Structural Basis of Poxvirus Transcription: Vaccinia RNA Polymerase Complexes.
Authors: Clemens Grimm / Hauke S Hillen / Kristina Bedenk / Julia Bartuli / Simon Neyer / Qian Zhang / Alexander Hüttenhofer / Matthias Erlacher / Christian Dienemann / Andreas Schlosser / Henning ...Authors: Clemens Grimm / Hauke S Hillen / Kristina Bedenk / Julia Bartuli / Simon Neyer / Qian Zhang / Alexander Hüttenhofer / Matthias Erlacher / Christian Dienemann / Andreas Schlosser / Henning Urlaub / Bettina Böttcher / Aladar A Szalay / Patrick Cramer / Utz Fischer /
Abstract: Poxviruses encode a multisubunit DNA-dependent RNA polymerase (vRNAP) that carries out viral gene expression in the host cytoplasm. We report cryo-EM structures of core and complete vRNAP enzymes ...Poxviruses encode a multisubunit DNA-dependent RNA polymerase (vRNAP) that carries out viral gene expression in the host cytoplasm. We report cryo-EM structures of core and complete vRNAP enzymes from Vaccinia virus at 2.8 Å resolution. The vRNAP core enzyme resembles eukaryotic RNA polymerase II (Pol II) but also reveals many virus-specific features, including the transcription factor Rap94. The complete enzyme additionally contains the transcription factor VETF, the mRNA processing factors VTF/CE and NPH-I, the viral core protein E11, and host tRNA. This complex can carry out the entire early transcription cycle. The structures show that Rap94 partially resembles the Pol II initiation factor TFIIB, that the vRNAP subunit Rpo30 resembles the Pol II elongation factor TFIIS, and that NPH-I resembles chromatin remodeling enzymes. Together with the accompanying paper (Hillen et al., 2019), these results provide the basis for unraveling the mechanisms of poxvirus transcription and RNA processing.
History
DepositionJan 20, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16476.png

Downloads & links

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Map

FileDownload / File: emd_16476.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo EM map of the complete vaccinia RNA polymerase lacking the capping enzyme
Projections & slices

Image control

Size
Brightness
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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

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.8152751 - 2.3454652
Average (Standard dev.)0.007679062 (±0.0606546)
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: Cryo EM map of the complete vaccinia RNA...

Fileemd_16476_half_map_1.map
AnnotationCryo EM map of the complete vaccinia RNA polymerase lacking the capping enzyme - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo EM map of the complete vaccinia RNA...

Fileemd_16476_half_map_2.map
AnnotationCryo EM map of the complete vaccinia RNA polymerase lacking the capping enzyme - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vaccinia complete RNA polymerase complex lacking the capping enzyme

EntireName: Vaccinia complete RNA polymerase complex lacking the capping enzyme
Components
  • Complex: Vaccinia complete RNA polymerase complex lacking the capping enzyme
    • Protein or peptide: DNA-directed RNA polymerase 133 kDa polypeptide
    • 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: RNA polymerase-associated transcription-specificity factor RAP94
    • Protein or peptide: DNA-directed RNA polymerase 7 kDa subunit
    • Protein or peptide: Core protein E11
    • Protein or peptide: Early transcription factor 82 kDa subunit
    • RNA: chr17.trna16-GlnTTG
    • Protein or peptide: DNA-directed RNA polymerase 147 kDa polypeptide
    • Protein or peptide: Nucleoside triphosphatase I
    • Protein or peptide: DNA-directed RNA polymerase 35 kDa subunit
    • Protein or peptide: DNA-directed RNA polymerase 30 kDa polypeptide
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Vaccinia complete RNA polymerase complex lacking the capping enzyme

SupramoleculeName: Vaccinia complete RNA polymerase complex lacking the capping enzyme
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: DNA-directed RNA polymerase 133 kDa polypeptide

MacromoleculeName: DNA-directed RNA polymerase 133 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 GLV-1h68
Molecular weightTheoretical: 133.526859 KDa
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 #2: DNA-directed RNA polymerase 22 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 22 kDa subunit / 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: 21.36574 KDa
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 #3: DNA-directed RNA polymerase 19 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 19 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: 19.020088 KDa
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 #4: DNA-directed RNA polymerase 18 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 18 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 GLV-1h68
Molecular weightTheoretical: 17.917195 KDa
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 #5: RNA polymerase-associated transcription-specificity factor RAP94

MacromoleculeName: RNA polymerase-associated transcription-specificity factor RAP94
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 93.667633 KDa
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 #6: DNA-directed RNA polymerase 7 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 7 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 GLV-1h68
Molecular weightTheoretical: 7.299715 KDa
SequenceString:
MVFQLVCSTC GKDISHERYK LIIRKKSLKD VLVSVKNECC RLKLSTQIEP QRNLTVQPLL DIN

UniProtKB: DNA-directed RNA polymerase 7 kDa subunit

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Macromolecule #7: Core protein E11

MacromoleculeName: Core protein E11 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 14.91409 KDa
SequenceString:
MELVNIFLET DAGRVKFAIK NTDDVCASEL INKFVELLSE YIHIDQSEFY LVVKDKDIFY FKCDRGSISI VNNEFYVFDE PLLFVKDFT NVTGVEFIVT ETMPCRIIPK NNHAVISVVT NHKFYNGLSL

UniProtKB: Core protein OPG073

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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 GLV-1h68
Molecular weightTheoretical: 82.398906 KDa
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 #10: DNA-directed RNA polymerase 147 kDa polypeptide

MacromoleculeName: DNA-directed RNA polymerase 147 kDa polypeptide / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 146.995703 KDa
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 #11: Nucleoside triphosphatase I

MacromoleculeName: Nucleoside triphosphatase I / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: nucleoside-triphosphate phosphatase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 72.46532 KDa
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 #12: DNA-directed RNA polymerase 35 kDa subunit

MacromoleculeName: DNA-directed RNA polymerase 35 kDa subunit / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 35.430676 KDa
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 #13: DNA-directed RNA polymerase 30 kDa polypeptide

MacromoleculeName: DNA-directed RNA polymerase 30 kDa polypeptide / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 30.074293 KDa
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

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Macromolecule #9: chr17.trna16-GlnTTG

MacromoleculeName: chr17.trna16-GlnTTG / type: rna / ID: 9 / Number of copies: 1
Source (natural)Organism: Vaccinia virus GLV-1h68
Molecular weightTheoretical: 23.10865 KDa
SequenceString:
GGUCCCAUGG UGUAAUGGUU AGCACUCUGG ACUUUGAAUC CAGCGAUCCG AGUUCAAAUC UCGGUGGGAC CU

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Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: water

MacromoleculeName: water / type: ligand / ID: 16 / Number of copies: 61 / 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

Concentration1 mg/mL
BufferpH: 7.4
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: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21338
FSC plot (resolution estimation)

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