3GZT | pdb_00003gzt

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 3GZT

This is version 2.1 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: 380.35 kDa 
  • Atom Count: 26,537 
  • Modeled Residue Count: 3,315 
  • Deposited Residue Count: 3,315 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer capsid glycoprotein VP7255Simian rotavirus A strain RRVMutation(s): 1 
UniProt
Find proteins for P12476 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Explore P12476 
Go to UniProtKB:  P12476
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12476
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N [auth A],
O [auth C],
P [auth D],
Q [auth E],
R,
N [auth A],
O [auth C],
P [auth D],
Q [auth E],
R,
S,
T,
U,
V,
W,
X,
Y,
Z
2N/A
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth Q]
BA [auth B]
BB [auth Q]
CA [auth B]
AA [auth B],
AB [auth Q],
BA [auth B],
BB [auth Q],
CA [auth B],
CB [auth Q],
DA [auth B],
DB [auth X],
EA [auth F],
FA [auth F],
GA [auth G],
HA [auth G],
IA [auth H],
JA [auth H],
KA [auth I],
LA [auth I],
MA [auth J],
NA [auth J],
OA [auth K],
PA [auth K],
QA [auth L],
RA [auth L],
SA [auth M],
TA [auth M],
UA [auth N],
VA [auth N],
WA [auth O],
XA [auth O],
YA [auth P],
ZA [auth P]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary