3GZU | pdb_00003gzu

VP7 recoated rotavirus DLP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 3GZU

This is version 1.4 of the entry. See complete history

Literature

Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM.

Chen, J.Z.Settembre, E.C.Aoki, S.T.Zhang, X.Bellamy, A.R.Dormitzer, P.R.Harrison, S.C.Grigorieff, N.

(2009) Proc Natl Acad Sci U S A 106: 10644-10648

  • DOI: https://doi.org/10.1073/pnas.0904024106
  • Primary Citation Related Structures: 
    3GZT, 3GZU

  • PubMed Abstract: 

    Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding.


  • Organizational Affiliation
    • Rosenstiel Basic Medical Research Center, Brandeis University, Waltham, MA 02454, USA.

Macromolecule Content 

  • Total Structure Weight: 770.02 kDa 
  • Atom Count: 53,996 
  • Modeled Residue Count: 6,742 
  • Deposited Residue Count: 6,761 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner capsid protein VP2
A, B
800Rotavirus AMutation(s): 0 
UniProt
Find proteins for B2BMD1 (Rotavirus A)
Explore B2BMD1 
Go to UniProtKB:  B2BMD1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2BMD1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Intermediate capsid protein VP6
C, D, E, F, G
C, D, E, F, G, H, I, J, K, L, M, N, O
397Simian rotavirus A strain RRVMutation(s): 0 
UniProt
Find proteins for P04509 (Rotavirus A (strain RVA/Cow/France/RF/1975/G6P6[1]))
Explore P04509 
Go to UniProtKB:  P04509
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04509
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 1.3: 2019-11-13
    Changes: Data collection, Other
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations