6RID | pdb_00006rid

Structure of Vaccinia Virus DNA-dependent RNA polymerase elongation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes.

Hillen, H.S.Bartuli, J.Grimm, C.Dienemann, C.Bedenk, K.Szalay, A.A.Fischer, U.Cramer, P.

(2019) Cell 179: 1525

  • DOI: https://doi.org/10.1016/j.cell.2019.11.023
  • Primary Citation Related Structures: 
    6RIC, 6RID, 6RIE

  • PubMed Abstract: 

    Poxviruses use virus-encoded multisubunit RNA polymerases (vRNAPs) and RNA-processing factors to generate m 7 G-capped mRNAs in the host cytoplasm. In the accompanying paper, we report structures of core and complete vRNAP complexes of the prototypic Vaccinia poxvirus (Grimm et al., 2019; in this issue of Cell). Here, we present the cryo-electron microscopy (cryo-EM) structures of Vaccinia vRNAP in the form of a transcribing elongation complex and in the form of a co-transcriptional capping complex that contains the viral capping enzyme (CE). The trifunctional CE forms two mobile modules that bind the polymerase surface around the RNA exit tunnel. RNA extends from the vRNAP active site through this tunnel and into the active site of the CE triphosphatase. Structural comparisons suggest that growing RNA triggers large-scale rearrangements on the surface of the transcription machinery during the transition from transcription initiation to RNA capping and elongation. Our structures unravel the basis for synthesis and co-transcriptional modification of poxvirus RNA.


  • Organizational Affiliation
    • Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 450.98 kDa 
  • Atom Count: 26,705 
  • Modeled Residue Count: 3,257 
  • Deposited Residue Count: 3,713 
  • Unique protein chains: 8
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-dependent RNA polymerase subunit rpo1471,286Vaccinia virus GLV-1h68Mutation(s): 0 
Gene Names: GL125
EC: 2.7.7.6
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-dependent RNA polymerase subunit rpo1321,164Vaccinia virus GLV-1h68Mutation(s): 0 
Gene Names: GL194
EC: 2.7.7.6
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 35 kDa subunit305Vaccinia virus GLV-1h68Mutation(s): 0 
Gene Names: GL205
EC: 2.7.7.6
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitD [auth E]185Vaccinia virus GLV-1h68Mutation(s): 0 
Gene Names: GL123
EC: 2.7.7.6
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 19 kDa subunitE [auth F]164Vaccinia virus GLV-1h68Mutation(s): 0 
Gene Names: GL167
EC: 2.7.7.6
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-dependent RNA polymerase subunit rpo18F [auth G]161Vaccinia virus GLV-1h68Mutation(s): 0 
Gene Names: GL147
EC: 2.7.7.6
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-dependent RNA polymerase subunit rpo7G [auth J]63Vaccinia virus GLV-1h68Mutation(s): 0 
Gene Names: GL107
EC: 2.7.7.6
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase 30 kDa polypeptideH [auth S]259Vaccinia virus GLV-1h68Mutation(s): 0 
Gene Names: GL076
EC: 2.7.7.6
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 9
MoleculeChains LengthOrganismImage
Non-template strand DNAI [auth N]48Orthopoxvirus vaccinia
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 10
MoleculeChains LengthOrganismImage
Template strand DNAJ [auth T]48Orthopoxvirus vaccinia
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 11
MoleculeChains LengthOrganismImage
RNAK [auth P]30Orthopoxvirus vaccinia
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB860
German Research FoundationGermanySPP1935
German Federal Ministry for Education and ResearchGermanyEXC 2067/1- 390729940
European Research CouncilGermanyTRANSREGULON
Volkswagen FoundationGermany--
German Research FoundationGermanyFi 573 7-2
German Research FoundationGermanyFi 573 18-1

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-12-17
    Changes: Data collection