3GZT

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


This is version 2.0 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 of 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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / 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		 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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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