3JB7

In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus.

Zhang, X.Ding, K.Yu, X.Chang, W.Sun, J.Hong Zhou, Z.

(2015) Nature 527: 531-534

  • DOI: 10.1038/nature15767
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Viruses in the Reoviridae, like the triple-shelled human rotavirus and the single-shelled insect cytoplasmic polyhedrosis virus (CPV), all package a genome of segmented double-stranded RNAs (dsRNAs) inside the viral capsid and carry out endogenous me ...

    Viruses in the Reoviridae, like the triple-shelled human rotavirus and the single-shelled insect cytoplasmic polyhedrosis virus (CPV), all package a genome of segmented double-stranded RNAs (dsRNAs) inside the viral capsid and carry out endogenous messenger RNA synthesis through a transcriptional enzyme complex (TEC). By direct electron-counting cryoelectron microscopy and asymmetric reconstruction, we have determined the organization of the dsRNA genome inside quiescent CPV (q-CPV) and the in situ atomic structures of TEC within CPV in both quiescent and transcribing (t-CPV) states. We show that the ten segmented dsRNAs in CPV are organized with ten TECs in a specific, non-symmetric manner, with each dsRNA segment attached directly to a TEC. The TEC consists of two extensively interacting subunits: an RNA-dependent RNA polymerase (RdRP) and an NTPase VP4. We find that the bracelet domain of RdRP undergoes marked conformational change when q-CPV is converted to t-CPV, leading to formation of the RNA template entry channel and access to the polymerase active site. An amino-terminal helix from each of two subunits of the capsid shell protein (CSP) interacts with VP4 and RdRP. These findings establish the link between sensing of environmental cues by the external proteins and activation of endogenous RNA transcription by the TEC inside the virus.


    Organizational Affiliation

    Bioengineering, University of California, Los Angeles, CA 90095, USA.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.,California Nanosystems Institute, Los Angeles, CA 90095, USA.,Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CPV RNA-dependent RNA polymerase
A
1225Bombyx mori cytoplasmic polyhedrosis virusMutation(s): 0 
Find proteins for D0EZK6 (Bombyx mori cytoplasmic polyhedrosis virus)
Go to UniProtKB:  D0EZK6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Viral structural protein 4
B
561Bombyx mori cytoplasmic polyhedrosis virusMutation(s): 0 
Find proteins for Q9IR43 (Bombyx mori cytoplasmic polyhedrosis virus)
Go to UniProtKB:  Q9IR43
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP1 CSP
C, D
24Bombyx mori cytoplasmic polyhedrosis virusMutation(s): 0 
Find proteins for D3JWE6 (Bombyx mori cytoplasmic polyhedrosis virus)
Go to UniProtKB:  D3JWE6
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*GP*GP*GP*GP*G)-3')t6Bombyx mori cypovirus 1
Entity ID: 5
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*CP*CP*CP*C)-3')m5Bombyx mori cypovirus 1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
CTP
Query on CTP

Download SDF File 
Download CCD File 
A
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references
  • Version 1.2: 2015-12-02
    Type: Database references
  • Version 1.3: 2018-07-18
    Type: Data collection