6QT9

Cryo-EM structure of SH1 full particle.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

Assembly of complex viruses exemplified by a halophilic euryarchaeal virus.

Colibus, L.Roine, E.Walter, T.S.Ilca, S.L.Wang, X.Wang, N.Roseman, A.M.Bamford, D.Huiskonen, J.T.Stuart, D.I.

(2019) Nat Commun 10: 1456-1456

  • DOI: https://doi.org/10.1038/s41467-019-09451-z
  • Primary Citation of Related Structures:  
    6QT9

  • PubMed Abstract: 

    Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). Here, by high-resolution cryo-EM analysis, we show that a class of archaeal viruses possess hetero-hexameric MCPs which mimic the PRD1-adeno lineage trimer. These hetero-hexamers are built from heterodimers and utilise a jigsaw-puzzle system of pegs and holes, and underlying minor capsid proteins, to assemble the capsid laterally from the 5-fold vertices. At these vertices proteins engage inwards with the internal membrane vesicle whilst 2-fold symmetric horn-like structures protrude outwards. The horns are assembled from repeated globular domains attached to a central spine, presumably facilitating multimeric attachment to the cell receptor. Such viruses may represent precursors of the main PRD1-adeno lineage, similarly engaging cell-receptors via 5-fold spikes and using minor proteins to define particle size.


  • Organizational Affiliation

    Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF 25A,
C [auth D]
226Haloarcula hispanica virus SH1Mutation(s): 0 
UniProt
Find proteins for Q4KPG2 (Haloarcula hispanica virus SH1)
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Go to UniProtKB:  Q4KPG2
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4KPG2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ORF 25225Haloarcula hispanica virus SH1Mutation(s): 0 
UniProt
Find proteins for Q4KPG2 (Haloarcula hispanica virus SH1)
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Go to UniProtKB:  Q4KPG2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4KPG2
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ORF 24173Haloarcula hispanica virus SH1Mutation(s): 0 
UniProt
Find proteins for Q4KPG3 (Haloarcula hispanica virus SH1)
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Go to UniProtKB:  Q4KPG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4KPG3
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ORF 24S [auth g],
X [auth l],
Z [auth n]
167Haloarcula hispanica virus SH1Mutation(s): 0 
UniProt
Find proteins for Q4KPG3 (Haloarcula hispanica virus SH1)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4KPG3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ORF 24T [auth h]175Haloarcula hispanica virus SH1Mutation(s): 0 
UniProt
Find proteins for Q4KPG3 (Haloarcula hispanica virus SH1)
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UniProt GroupQ4KPG3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ORF 31BA [auth Y]135Haloarcula hispanica virus SH1Mutation(s): 0 
UniProt
Find proteins for Q4KPF6 (Haloarcula hispanica virus SH1)
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Go to UniProtKB:  Q4KPF6
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UniProt GroupQ4KPF6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
VP12CA [auth X]24Haloarcula hispanica virus SH1Mutation(s): 0 
Sequence Annotations
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
VP13DA [auth W]80Haloarcula hispanica virus SH1Mutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM
MODEL REFINEMENTPHENIX1.14_3260

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N00065X/1
European Research CouncilUnited Kingdom649053
Academy of FinlandFinland255342
Academy of FinlandFinland256518

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.2: 2019-11-27
    Changes: Data collection
  • Version 1.3: 2019-12-18
    Changes: Other