3JB0

Atomic model of cytoplasmic polyhedrosis virus with GTP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A putative ATPase mediates RNA transcription and capping in a dsRNA virus.

Yu, X.Jiang, J.Sun, J.Zhou, Z.H.

(2015) Elife 4: e07901-e07901

  • DOI: 10.7554/eLife.07901
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high-resolution (2.9-3.1 Å) cryo-electron microscopy structu ...

    mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high-resolution (2.9-3.1 Å) cryo-electron microscopy structures of cytoplasmic polyhedrosis virus with bound ligands, we show that the large sub-domain of the guanylyltransferase (GTase) domain of the turret protein (TP) also has an ATP-binding site and is likely an ATPase. S-adenosyl-L-methionine (SAM) acts as a signal and binds the methylase-2 domain of TP to induce conformational change of the viral capsid, which in turn activates the putative ATPase. ATP binding/hydrolysis leads to an enlarged capsid for efficient mRNA synthesis, an open GTase domain for His217-mediated guanylyl transfer, and an open methylase-1 domain for SAM binding and methyl transfer. Taken together, our data support a role of the putative ATPase in mediating the activation of mRNA transcription and capping within the confines of the virus.


    Organizational Affiliation

    Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Structural protein VP3
A
1058Bombyx mori cytoplasmic polyhedrosis virusMutation(s): 0 
Find proteins for Q914N6 (Bombyx mori cytoplasmic polyhedrosis virus)
Go to UniProtKB:  Q914N6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
B, C
1333Bombyx mori cytoplasmic polyhedrosis virusMutation(s): 0 
Find proteins for Q6TS43 (Bombyx mori cytoplasmic polyhedrosis virus)
Go to UniProtKB:  Q6TS43
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Viral structural protein 5
D, E
448Bombyx mori cytoplasmic polyhedrosis virusMutation(s): 0 
Gene Names: VP5
Find proteins for C6K2M8 (Bombyx mori cytoplasmic polyhedrosis virus)
Go to UniProtKB:  C6K2M8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 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: 2015-08-12
    Type: Initial release
  • Version 1.1: 2016-11-02
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection