4V7Q | pdb_00004v7q

Atomic model of an infectious rotavirus particle

• PDB DOI: https://doi.org/10.2210/pdb4V7Q/pdb
• Entry: 4V7Q supersedes: 3IYU, 3N09
• EM Map EMD-5199: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Simian rotavirus A strain RRV
• Expression System: Chlorocebus sabaeus
• Mutation(s): No 


• Deposited: 2010-05-13 Released: 2014-07-09 
• Deposition Author(s): Settembre, E.C., Chen, J.Z., Dormitzer, P.R., Grigorieff, N., Harrison, S.C.

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Experimental Data Snapshot

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

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

• PubMed: 21157433 
• DOI: https://doi.org/10.1038/emboj.2010.322
• Primary Citation Related Structures: 
  4V7Q


• 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 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.

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Organizational Affiliation: 
• Laboratory of Molecular Medicine, Children's Hospital, Boston, MA, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 1860-mer - A780B780C120D120E60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 1860-mer - A780B780C120D60E60F60 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 1,440.04 kDa 
• Atom Count: 97,287 
• Modeled Residue Count: 12,198 
• Deposited Residue Count: 12,677 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Core scaffold protein	A [auth AA], B [auth AB]	800	Simian rotavirus A strain RRV	Mutation(s): 0  Gene Names: Rotavirus
UniProt
Find proteins for B3F2X3 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])) Explore B3F2X3  Go to UniProtKB:  B3F2X3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Intermediate capsid protein VP6	C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], H [auth AH], I [auth AI], J [auth AJ], K [auth AK], L [auth AL], M [auth AM], N [auth AN], O [auth AO]	397	Simian rotavirus A strain RRV	Mutation(s): 0  Gene Names: Rotavirus
UniProt
Find proteins for B2BN53 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])) Explore B2BN53  Go to UniProtKB:  B2BN53

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer layer protein VP7	AA [auth BP], BA [auth BQ], P [auth BA], Q [auth BF], R [auth BG], S [auth BH], T [auth BI], U [auth BJ], V [auth BK], W [auth BL], X [auth BM], Y [auth BN], Z [auth BO]	276	Simian rotavirus A strain RRV	Mutation(s): 0
UniProt
Find proteins for P12476 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])) Explore P12476  Go to UniProtKB:  P12476
Glycosylation
Glycosylation Sites: 1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP4	CA [auth BX], DA [auth BY], EA [auth BZ]	776	Simian rotavirus A strain RRV	Mutation(s): 0
UniProt
Find proteins for C3RX20 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])) Explore C3RX20  Go to UniProtKB:  C3RX20

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth A], GA [auth B], HA [auth C], IA [auth D], JA [auth E], KA [auth F], LA [auth G]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	RA [auth BM]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	MA [auth AC], NA [auth AF], OA [auth AK], PA [auth AN], QA [auth AO]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Settembre, E.C., Chen, J.Z., Dormitzer, P.R., Grigorieff, N., Harrison, S.C.
• This entry supersedes: 3IYU, 3N09

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Other
• Version 1.2: 2018-01-24
  Changes: Data collection, Structure summary
• Version 1.3: 2019-12-18
  Changes: Database references, Derived calculations, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary