6TY8 | pdb_00006ty8

In situ structure of BmCPV RNA dependent RNA polymerase at quiescent state

  • Classification: VIRAL PROTEIN, TRANSFERASE
  • Organism(s): Bombyx mori cypovirus 1
  • Mutation(s): No 

  • Deposited: 2019-08-08 Released: 2019-11-20 
  • Deposition Author(s): Cui, Y.X., Zhang, Y.N., Sun, J.C., Zhou, Z.H.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Institutes of Health/Office of the Director, National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6TY8

This is version 1.3 of the entry. See complete history

Literature

Conservative transcription in three steps visualized in a double-stranded RNA virus.

Cui, Y.Zhang, Y.Zhou, K.Sun, J.Zhou, Z.H.

(2019) Nat Struct Mol Biol 26: 1023-1034

  • DOI: https://doi.org/10.1038/s41594-019-0320-0
  • Primary Citation Related Structures: 
    6TY8, 6TY9, 6TZ0, 6TZ1, 6TZ2

  • PubMed Abstract: 

    Endogenous RNA transcription characterizes double-stranded RNA (dsRNA) viruses in the Reoviridae, a family that is exemplified by its simple, single-shelled member cytoplasmic polyhedrosis virus (CPV). Because of the lack of in situ structures of the intermediate stages of RNA-dependent RNA polymerase (RdRp) during transcription, it is poorly understood how RdRp detects environmental cues and internal transcriptional states to initiate and coordinate repeated cycles of transcript production inside the capsid. Here, we captured five high-resolution (2.8-3.5 Å) RdRp-RNA in situ structures-representing quiescent, initiation, early elongation, elongation and abortive states-under seven experimental conditions of CPV. We observed the 'Y'-form initial RNA fork in the initiation state and the complete transcription bubble in the elongation state. These structures reveal that de novo RNA transcription involves three major conformational changes during state transitions. Our results support an ouroboros model for endogenous conservative transcription in dsRNA viruses.


  • Organizational Affiliation
    • California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 203.48 kDa 
  • Atom Count: 13,607 
  • Modeled Residue Count: 1,694 
  • Deposited Residue Count: 1,786 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-dependent RNA Polymerase1,225Bombyx mori cypovirus 1Mutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for Q993A4 (Bombyx mori cytoplasmic polyhedrosis virus)
Explore Q993A4 
Go to UniProtKB:  Q993A4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ993A4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Viral structural protein 4561Bombyx mori cypovirus 1Mutation(s): 0 
UniProt
Find proteins for Q9IR43 (Bombyx mori cytoplasmic polyhedrosis virus)
Explore Q9IR43 
Go to UniProtKB:  Q9IR43
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IR43
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTA

Query on GTA



Download:Ideal Coordinates CCD File
C [auth A]P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
C21 H30 N10 O17 P3
QQOHNVHGNZYSBP-XPWFQUROSA-O

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31672489
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM071940
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States1S10RR23057
National Institutes of Health/Office of the DirectorUnited States1S10OD018111
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM116792
National Science Foundation (NSF, United States)United StatesDMR-1548924
National Science Foundation (NSF, United States)United StatesDBI-1338135

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references
  • Version 1.3: 2025-06-04
    Changes: Data collection, Structure summary