6IUK

Cryo-EM structure of Murine Norovirus capsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dynamic rotation of the protruding domain enhances the infectivity of norovirus.

Song, C.Takai-Todaka, R.Miki, M.Haga, K.Fujimoto, A.Ishiyama, R.Oikawa, K.Yokoyama, M.Miyazaki, N.Iwasaki, K.Murakami, K.Katayama, K.Murata, K.

(2020) PLoS Pathog 16: e1008619-e1008619

  • DOI: https://doi.org/10.1371/journal.ppat.1008619
  • Primary Citation of Related Structures:  
    6IUK

  • PubMed Abstract: 

    Norovirus is the major cause of epidemic nonbacterial gastroenteritis worldwide. Lack of structural information on infection and replication mechanisms hampers the development of effective vaccines and remedies. Here, using cryo-electron microscopy, we show that the capsid structure of murine noroviruses changes in response to aqueous conditions. By twisting the flexible hinge connecting two domains, the protruding (P) domain reversibly rises off the shell (S) domain in solutions of higher pH, but rests on the S domain in solutions of lower pH. Metal ions help to stabilize the resting conformation in this process. Furthermore, in the resting conformation, the cellular receptor CD300lf is readily accessible, and thus infection efficiency is significantly enhanced. Two similar P domain conformations were also found simultaneously in the human norovirus GII.3 capsid, although the mechanism of the conformational change is not yet clear. These results provide new insights into the mechanisms of non-enveloped norovirus transmission that invades host cells, replicates, and sometimes escapes the hosts immune system, through dramatic environmental changes in the gastrointestinal tract.


  • Organizational Affiliation

    National Institute for Physiological Sciences, Okazaki, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein VP1
A, B, C
541Murine norovirus GV/NIH-2410/2005/USAMutation(s): 0 
Gene Names: VP1
UniProt
Find proteins for B7XA03 (Murine norovirus)
Explore B7XA03 
Go to UniProtKB:  B7XA03
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7XA03
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13
RECONSTRUCTIONRELION2.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP18fk0108034h0602
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101072j0001
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP26102545
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP16H00786

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations