5GKA

cryo-EM structure of human Aichi virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of human Aichi virus and implications for receptor binding

Zhu, L.Wang, X.Ren, J.Kotecha, A.Walter, T.S.Yuan, S.Yamashita, T.Tuthill, T.J.Fry, E.E.Rao, Z.Stuart, D.I.

(2016) Nat Microbiol 1: 16150-16150

  • DOI: https://doi.org/10.1038/nmicrobiol.2016.150
  • Primary Citation of Related Structures:  
    5GKA

  • PubMed Abstract: 

    Aichi virus (AiV), an unusual and poorly characterized picornavirus, classified in the genus Kobuvirus, can cause severe gastroenteritis and deaths in children below the age of five years, especially in developing countries 1,2 . The seroprevalence of AiV is approximately 60% in children under the age of ten years and reaches 90% later in life 3,4 . There is no available vaccine or effective antiviral treatment. Here, we describe the structure of AiV at 3.7 Å. This first high-resolution structure for a kobuvirus is intermediate between those of the enteroviruses and cardioviruses, with a shallow, narrow depression bounded by the prominent VP0 CD loops (linking the C and D strands of the β-barrel), replacing the depression known as the canyon, frequently the site of receptor attachment in enteroviruses. VP0 is not cleaved to form VP2 and VP4, so the 'VP2' β-barrel structure is complemented with a unique extended structure on the inside of the capsid. On the outer surface, a polyproline helix structure, not seen previously in picornaviruses is present at the C terminus of VP1, a position where integrin binding motifs are found in some other picornaviruses. A peptide corresponding to this polyproline motif somewhat attenuates virus infectivity, presumably blocking host-cell attachment. This may guide cellular receptor identification.


  • Organizational Affiliation

    Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein VP1253Aichi virus A846/88Mutation(s): 0 
UniProt
Find proteins for O91464 (Aichi virus (strain Human/A846/88/1989))
Explore O91464 
Go to UniProtKB:  O91464
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO91464
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein VP0367Aichi virus A846/88Mutation(s): 0 
UniProt
Find proteins for O91464 (Aichi virus (strain Human/A846/88/1989))
Explore O91464 
Go to UniProtKB:  O91464
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO91464
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein222Aichi virus A846/88Mutation(s): 0 
UniProt
Find proteins for O91464 (Aichi virus (strain Human/A846/88/1989))
Explore O91464 
Go to UniProtKB:  O91464
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO91464
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.3
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyChina2014CB542800
Medical Research Council (United Kingdom)United KingdomG100099

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Source and taxonomy
  • Version 1.2: 2017-04-26
    Changes: Other, Source and taxonomy
  • Version 1.3: 2017-10-18
    Changes: Author supporting evidence, Data processing
  • Version 1.4: 2024-03-27
    Changes: Data collection, Database references, Derived calculations