3J17

Structure of a transcribing cypovirus by cryo-electron microscopy


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 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

Cryo-EM structure of a transcribing cypovirus.

Yang, C.Ji, G.Liu, H.Zhang, K.Liu, G.Sun, F.Zhu, P.Cheng, L.

(2012) Proc.Natl.Acad.Sci.USA 109: 6118-6123

  • DOI: 10.1073/pnas.1200206109

  • PubMed Abstract: 
  • Double-stranded RNA viruses in the family Reoviridae are capable of transcribing and capping nascent mRNA within an icosahedral viral capsid that remains intact throughout repeated transcription cycles. However, how the highly coordinated mRNA transc ...

    Double-stranded RNA viruses in the family Reoviridae are capable of transcribing and capping nascent mRNA within an icosahedral viral capsid that remains intact throughout repeated transcription cycles. However, how the highly coordinated mRNA transcription and capping process is facilitated by viral capsid proteins is still unknown. Cypovirus provides a good model system for studying the mRNA transcription and capping mechanism of viruses in the family Reoviridae. Here, we report a full backbone model of a transcribing cypovirus built from a near-atomic-resolution density map by cryoelectron microscopy. Compared with the structure of a nontranscribing cypovirus, the major capsid proteins of transcribing cypovirus undergo a series of conformational changes, giving rise to structural changes in the capsid shell: (i) an enlarged capsid chamber, which provides genomic RNA with more flexibility to move within the densely packed capsid, and (ii) a widened peripentonal channel in the capsid shell, which we confirmed to be a pathway for nascent mRNA. A rod-like structure attributable to a partially resolved nascent mRNA was observed in this channel. In addition, conformational change in the turret protein results in a relatively open turret at each fivefold axis. A GMP moiety, which is transferred to 5'-diphosphorylated mRNA during the mRNA capping reaction, was identified in the pocket-like guanylyltransferase domain of the turret protein.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.




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
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
Structural protein VP5
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GPL
Query on GPL
A
L-PEPTIDE LINKINGC16 H26 N7 O9 PLYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 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: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection