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 7XR2 | pdb_00007xr2

3.1 Angstrom cryoEM icosahedral reconstruction of mud crab reovirus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7XR2

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 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.

Macromolecule Content 

  • Total Structure Weight: 628.04 kDa 
  • Atom Count: 43,557 
  • Modeled Residue Count: 5,608 
  • Deposited Residue Count: 5,676 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VP3
A, B
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
VP11C [auth 1],
D [auth 2]
203Scylla serrata reovirus SZ-2007Mutation(s): 0 
UniProt
Find proteins for G9BDA7 (Scylla serrata reovirus SZ-2007)
Explore G9BDA7 
Go to UniProtKB:  G9BDA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9BDA7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VP12274Scylla serrata reovirus SZ-2007Mutation(s): 0 
UniProt
Find proteins for G9BDA8 (Scylla serrata reovirus SZ-2007)
Explore G9BDA8 
Go to UniProtKB:  G9BDA8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9BDA8
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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: 2025-06-25
    Changes: Data collection, Structure summary