8RQK

Structure of the complete Vaccinia DNA-dependent RNA polymerase complex at 2.65A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of the complete Vaccinia DNA-dependent RNA polymerase complex at 2.65A resolution

Grimm, C.Bartuli, J.Fischer, U.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 147 kDa polypeptide1,286Vaccinia virusMutation(s): 3 
Gene Names: OPG105RPO147J6R
EC: 2.7.7.6
UniProt
Find proteins for P20504 (Vaccinia virus (strain Copenhagen))
Explore P20504 
Go to UniProtKB:  P20504
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20504
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 133 kDa polypeptide1,164Vaccinia virusMutation(s): 2 
Gene Names: OPG151RPO132A24R
EC: 2.7.7.6
UniProt
Find proteins for P68694 (Vaccinia virus (strain Copenhagen))
Explore P68694 
Go to UniProtKB:  P68694
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68694
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 35 kDa subunit305Vaccinia virusMutation(s): 1 
Gene Names: OPG156RPO35A29L
EC: 2.7.7.6
UniProt
Find proteins for P21087 (Vaccinia virus (strain Copenhagen))
Explore P21087 
Go to UniProtKB:  P21087
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21087
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 22 kDa subunitD [auth E]185Vaccinia virusMutation(s): 0 
Gene Names: OPG103RPO22J4R
EC: 2.7.7.6
UniProt
Find proteins for P68608 (Vaccinia virus (strain Copenhagen))
Explore P68608 
Go to UniProtKB:  P68608
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68608
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 18 kDa subunitE [auth G]161Vaccinia virusMutation(s): 0 
Gene Names: OPG119RPO18D7R
EC: 2.7.7.6
UniProt
Find proteins for P21034 (Vaccinia virus (strain Copenhagen))
Explore P21034 
Go to UniProtKB:  P21034
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21034
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated transcription-specificity factor RAP94F [auth I]795Vaccinia virusMutation(s): 0 
Gene Names: OPG109RAP94H4L
UniProt
Find proteins for P68439 (Vaccinia virus (strain Copenhagen))
Explore P68439 
Go to UniProtKB:  P68439
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68439
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 7 kDa subunitG [auth J]63Vaccinia virusMutation(s): 0 
Gene Names: OPG090RPO7G5.5R
EC: 2.7.7.6
UniProt
Find proteins for P68315 (Vaccinia virus (strain Copenhagen))
Explore P68315 
Go to UniProtKB:  P68315
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68315
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Early transcription factor 82 kDa subunitH [auth K]710Vaccinia virusMutation(s): 1 
Gene Names: OPG133VETFLA7L
UniProt
Find proteins for P20635 (Vaccinia virus (strain Copenhagen))
Explore P20635 
Go to UniProtKB:  P20635
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20635
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA-capping enzyme regulatory subunit OPG124I [auth L]287Vaccinia virusMutation(s): 1 
Gene Names: OPG124D12L
UniProt
Find proteins for P20980 (Vaccinia virus (strain Copenhagen))
Explore P20980 
Go to UniProtKB:  P20980
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20980
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA-capping enzyme catalytic subunitJ [auth O]844Vaccinia virusMutation(s): 2 
Gene Names: OPG113D1R
EC: 3.6.1.74 (PDB Primary Data), 2.7.7.50 (PDB Primary Data), 2.1.1.56 (PDB Primary Data)
UniProt
Find proteins for P20979 (Vaccinia virus (strain Copenhagen))
Explore P20979 
Go to UniProtKB:  P20979
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20979
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein OPG073K [auth Q],
L [auth R]
129Vaccinia virusMutation(s): 0 
Gene Names: OPG073E11L
UniProt
Find proteins for P68449 (Vaccinia virus (strain Copenhagen))
Explore P68449 
Go to UniProtKB:  P68449
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68449
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 30 kDa polypeptideM [auth S]259Vaccinia virusMutation(s): 0 
Gene Names: OPG066RPO30E4L
EC: 2.7.7.6
UniProt
Find proteins for P21082 (Vaccinia virus (strain Copenhagen))
Explore P21082 
Go to UniProtKB:  P21082
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21082
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside triphosphatase IO [auth Y]631Vaccinia virusMutation(s): 1 
Gene Names: OPG123NPH1D11L
EC: 3.6.1.15
UniProt
Find proteins for P20637 (Vaccinia virus (strain Copenhagen))
Explore P20637 
Go to UniProtKB:  P20637
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20637
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 19 kDa subunitP [auth F]164Vaccinia virusMutation(s): 0 
Gene Names: OPG131RPO19A5R
EC: 2.7.7.6
UniProt
Find proteins for P68610 (Vaccinia virus (strain Copenhagen))
Explore P68610 
Go to UniProtKB:  P68610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68610
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
R [auth A],
S [auth A],
T [auth B],
U [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
Q [auth A],
V [auth U],
W [auth U],
X [auth U]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
M [auth S]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5058

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release