7XR3 | pdb_00007xr3

3.4 Angstrom cryoEM D5 reconstruction of mud crab reovirus


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 1.3 of the entry. See complete history


Literature

The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization.

Zhang, Q.Gao, Y.Baker, M.L.Liu, S.Jia, X.Xu, H.He, J.Kaelber, J.T.Weng, S.Jiang, W.

(2023) PLoS Pathog 19: e1011341-e1011341

  • DOI: https://doi.org/10.1371/journal.ppat.1011341
  • Primary Citation of Related Structures:  
    7XR2, 7XR3

  • PubMed Abstract: 

    Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses.


  • Organizational Affiliation
    • State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP3
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
854Scylla serrata reovirus SZ-2007Mutation(s): 0 
UniProt
Find proteins for E9LEU6 (Scylla serrata reovirus SZ-2007)
Explore E9LEU6 
Go to UniProtKB:  E9LEU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9LEU6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP1K [auth Z]1,425Scylla serrata reovirus SZ-2007Mutation(s): 0 
UniProt
Find proteins for G9BD97 (Scylla serrata reovirus SZ-2007)
Explore G9BD97 
Go to UniProtKB:  G9BD97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9BD97
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
MODEL REFINEMENTPHENIX
RECONSTRUCTIONjspr2014

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31570736
National Natural Science Foundation of China (NSFC)China31672677

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2024-07-03
    Changes: Data collection
  • Version 1.3: 2025-07-02
    Changes: Data collection, Structure summary