4V7Q

Atomic model of an infectious rotavirus particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 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

Atomic model of an infectious rotavirus particle.

Settembre, E.C.Chen, J.Z.Dormitzer, P.R.Grigorieff, N.Harrison, S.C.

(2011) Embo J. 30: 408-416

  • DOI: 10.1038/emboj.2010.322
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to confo ...

    Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus-penetration protein, and infectivity analyses of structure-based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single-particle analysis at about 4.3 Å resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8(*) and VP5(*)) retain their association after proteolytic cleavage, reveals multiple structural roles for the β-barrel domain of VP5(*), and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry.


    Organizational Affiliation

    Laboratory of Molecular Medicine, Children's Hospital, Boston, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Core scaffold protein
AA, AB
800Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])Mutation(s): 0 
Find proteins for B3F2X3 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Go to UniProtKB:  B3F2X3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Intermediate capsid protein VP6
AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO
397Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])Mutation(s): 0 
Find proteins for B2BN53 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Go to UniProtKB:  B2BN53
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Outer layer protein VP7
BA, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ
276Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])Mutation(s): 0 
Find proteins for P12476 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Go to UniProtKB:  P12476
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Outer capsid protein VP4
BX, BY, BZ
776Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])Mutation(s): 0 
Find proteins for C3RX20 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Go to UniProtKB:  C3RX20
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
AC, AF, AK, AN, AO
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
BA, BF, BH, BI, BM, BN, BO, BQ
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 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: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2018-01-24
    Type: Data collection, Structure summary