3K1Q

Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Backbone Model of an Aquareovirus Virion by Cryo-Electron Microscopy and Bioinformatics

Cheng, L.Zhu, J.Hui, W.H.Zhang, X.Honig, B.Fang, Q.Zhou, Z.H.

(2010) J Mol Biol 397: 852-863

  • DOI: 10.1016/j.jmb.2009.12.027
  • Primary Citation of Related Structures:  
    3K1Q

  • PubMed Abstract: 
  • Grass carp reovirus (GCRV) is a member of the aquareovirus genus in the Reoviridae family and has a capsid with two shells-a transcription-competent core surrounded by a coat. We report a near-atomic-resolution reconstruction of the GCRV virion by cryo-electron microscopy and single-particle reconstruction ...

    Grass carp reovirus (GCRV) is a member of the aquareovirus genus in the Reoviridae family and has a capsid with two shells-a transcription-competent core surrounded by a coat. We report a near-atomic-resolution reconstruction of the GCRV virion by cryo-electron microscopy and single-particle reconstruction. A backbone model of the GCRV virion, including seven conformers of the five capsid proteins making up the 1500 molecules in both the core and the coat, was derived using cryo-electron microscopy density-map-constrained homology modeling and refinement. Our structure clearly showed that the amino-terminal segment of core protein VP3B forms an approximately 120-A-long alpha-helix-rich extension bridging across the icosahedral 2-fold-symmetry-related molecular interface. The presence of this unique structure across this interface and the lack of an external cementing molecule at this location in GCRV suggest a stabilizing role of this extended amino-terminal density. Moreover, part of this amino-terminal extension becomes invisible in the reconstruction of transcription-competent core particles, suggesting its involvement in endogenous viral RNA transcription. Our structure of the VP1 turret represents its open state, and comparison with its related structures at the closed state suggests hinge-like domain movements associated with the mRNA-capping machinery. Overall, this first backbone model of an aquareovirus virion provides a wealth of structural information for understanding the structural basis of GCRV assembly and transcription.


    Related Citations: 
    • Building Models for Molecular Assemblies by Cryo-electron Microscopy, Homology Modeling and Multi-scale Structure-Based Refinement
      Honig, B.
      () To be published --: --

    Organizational Affiliation

    Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA 90095-7364, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP1A1,299Grass carp reovirusMutation(s): 0 
UniProt
Find proteins for Q9E3W0 (Grass carp reovirus)
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Go to UniProtKB:  Q9E3W0
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UniProt GroupQ9E3W0
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VP3AB1,027Grass carp reovirusMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for Q9E3V8 (Grass carp reovirus)
Explore Q9E3V8 
Go to UniProtKB:  Q9E3V8
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UniProt GroupQ9E3V8
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VP3BC1,196Grass carp reovirusMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for Q9E3V8 (Grass carp reovirus)
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UniProt GroupQ9E3V8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Core protein VP6D, E412Grass carp reovirusMutation(s): 0 
UniProt
Find proteins for Q8JU64 (Grass carp reovirus)
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UniProt GroupQ8JU64
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Outer capsid VP7
F, G, H, L, M, N, R, S, T, Y
F, G, H, L, M, N, R, S, T, Y
276Grass carp reovirusMutation(s): 0 
UniProt
Find proteins for Q8JU63 (Grass carp reovirus)
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UniProt GroupQ8JU63
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Outer capsid VP5
I, J, K, O, P, Q, U, V, W, X
I, J, K, O, P, Q, U, V, W, X
639Grass carp reovirusMutation(s): 0 
UniProt
Find proteins for Q8JU67 (Grass carp reovirus)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-01-14
    Changes: Database references, Other