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- PDB-9fpy: Structure of the complete Vaccinia DNA-dependent RNA polymerase c... -

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Basic information

Entry
Database: PDB / ID: 9fpy
TitleStructure of the complete Vaccinia DNA-dependent RNA polymerase complex assembly intermediate 3
Components
  • (DNA-directed RNA polymerase ...) x 8
  • Core protein OPG073
  • Nucleoside triphosphatase I
  • RNA polymerase-associated transcription-specificity factor RAP94
  • URQ-UUG1-1 tRNA (72-MER)
KeywordsTRANSCRIPTION / VACCINIA / RNA POLYMERASE / RNA POLYMERASE COMPLEX / RNAP / VRNAP / COMPLETE VRNAP / VIRAL PROTEIN
Function / homology
Function and homology information


viral transcription / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / ribonucleoside triphosphate phosphatase activity / DNA-templated transcription termination / ribonucleoside binding / virion component / : / : / : ...viral transcription / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / ribonucleoside triphosphate phosphatase activity / DNA-templated transcription termination / ribonucleoside binding / virion component / : / : / : / : / : / : / DNA-directed RNA polymerase / nucleoside-triphosphate phosphatase / host cell cytoplasm / DNA-binding transcription factor activity / DNA-templated transcription / DNA binding / zinc ion binding / ATP binding / metal ion binding
Similarity search - Function
Virion core protein, vaccinia E11L type / Nucleoside triphosphatase I, C-terminal / Chordopoxvirus E11 protein / 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 ...Virion core protein, vaccinia E11L type / Nucleoside triphosphatase I, C-terminal / Chordopoxvirus E11 protein / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / DNA-directed RNA polymerase 147 kDa polypeptide / Nucleoside triphosphatase I / 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 ...RNA / RNA (> 10) / DNA-directed RNA polymerase 147 kDa polypeptide / Nucleoside triphosphatase I / 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 133 kDa polypeptide / DNA-directed RNA polymerase 19 kDa subunit
Similarity search - Component
Biological speciesOrthopoxvirus vaccinia
Vaccinia virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsGrimm, C. / Bartuli, J. / Fischer, U.
Funding support Germany, 1items
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
DepositionJun 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA-directed RNA polymerase 35 kDa subunit
E: DNA-directed RNA polymerase 22 kDa subunit
G: DNA-directed RNA polymerase 18 kDa subunit
J: DNA-directed RNA polymerase 7 kDa subunit
Q: Core protein OPG073
R: Core protein OPG073
U: URQ-UUG1-1 tRNA (72-MER)
A: DNA-directed RNA polymerase 147 kDa polypeptide
B: DNA-directed RNA polymerase 133 kDa polypeptide
F: DNA-directed RNA polymerase 19 kDa subunit
I: RNA polymerase-associated transcription-specificity factor RAP94
S: DNA-directed RNA polymerase 30 kDa polypeptide
Y: Nucleoside triphosphatase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)631,10121
Polymers630,74213
Non-polymers3598
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA-directed RNA polymerase ... , 8 types, 8 molecules CEGJABFS

#1: Protein DNA-directed RNA polymerase 35 kDa subunit


Mass: 35430.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG156, RPO35, A29L / Production host: Vaccinia virus / References: UniProt: P21087, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase 22 kDa subunit


Mass: 21365.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG103, RPO22, J4R / Production host: Vaccinia virus / References: UniProt: P68608, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase 18 kDa subunit


Mass: 17917.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG119, RPO18, D7R / Production host: Vaccinia virus / References: UniProt: P21034, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase 7 kDa subunit


Mass: 7299.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG090, RPO7, G5.5R / Production host: Vaccinia virus / References: UniProt: P68315, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase 147 kDa polypeptide


Mass: 146995.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG105, RPO147, J6R / Production host: Vaccinia virus / References: UniProt: P20504, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase 133 kDa polypeptide


Mass: 133526.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG151, RPO132, A24R / Production host: Vaccinia virus / References: UniProt: P68694, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase 19 kDa subunit


Mass: 19020.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG131, RPO19, MVA116R, ACAM3000_MVA_116, A5R / Production host: Vaccinia virus / References: UniProt: Q76ZQ8, DNA-directed RNA polymerase
#11: Protein DNA-directed RNA polymerase 30 kDa polypeptide


Mass: 30074.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG066, RPO30, E4L / Production host: Vaccinia virus / References: UniProt: P21082, DNA-directed RNA polymerase

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Protein , 3 types, 4 molecules QRIY

#5: Protein Core protein OPG073 / Protein E11


Mass: 14914.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG073, E11L / Production host: Vaccinia virus / References: UniProt: P68449
#10: Protein RNA polymerase-associated transcription-specificity factor RAP94 / Protein H4 / RPO-associated protein of 94 kDa


Mass: 93667.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG109, RAP94, H4L / Production host: Vaccinia virus / References: UniProt: P68439
#12: Protein Nucleoside triphosphatase I / Factor X / NPH-I / Nucleoside triphosphate phosphohydrolase I / NPH I


Mass: 72465.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG123, NPH1, D11L / Production host: Vaccinia virus
References: UniProt: P20637, nucleoside-triphosphate phosphatase

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RNA chain , 1 types, 1 molecules U

#6: RNA chain URQ-UUG1-1 tRNA (72-MER)


Mass: 23150.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Production host: Vaccinia virus

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Non-polymers , 3 types, 17 molecules

#13: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: complete Vaccinia DNA-dependent RNA polymerase complex
Type: COMPLEX / Entity ID: #1-#12 / Source: RECOMBINANT
Molecular weightValue: 0.87 MDa / Experimental value: YES
Source (natural)Organism: Vaccinia virus
Source (recombinant)Organism: Vaccinia virus
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 70 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
9PHENIX1.21rc1_5058model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96385 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6rfl

6rfl


Accession code: 6rfl / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 88.84 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002641996
ELECTRON MICROSCOPYf_angle_d0.490157132
ELECTRON MICROSCOPYf_chiral_restr0.04176539
ELECTRON MICROSCOPYf_plane_restr0.00316948
ELECTRON MICROSCOPYf_dihedral_angle_d7.7486174

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