6H9C

Cryo-EM structure of archaeal extremophilic internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) at 3.74 Angstroms resolution.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.74 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

Structural basis for assembly of vertical single beta-barrel viruses.

Santos-Perez, I.Charro, D.Gil-Carton, D.Azkargorta, M.Elortza, F.Bamford, D.H.Oksanen, H.M.Abrescia, N.G.A.

(2019) Nat Commun 10: 1184-1184

  • DOI: https://doi.org/10.1038/s41467-019-08927-2
  • Primary Citation of Related Structures:  
    6H82, 6H9C

  • PubMed Abstract: 

    The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs.


  • Organizational Affiliation

    Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP7184Haloarcula californiae ATCC 33799Mutation(s): 0 
UniProt
Find proteins for A0A1C7A3R1 (Haloarcula californiae icosahedral virus 1)
Explore A0A1C7A3R1 
Go to UniProtKB:  A0A1C7A3R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7A3R1
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP9B [auth b]146Haloarcula californiae ATCC 33799Mutation(s): 0 
UniProt
Find proteins for A0A1C7A3R7 (Haloarcula californiae icosahedral virus 1)
Explore A0A1C7A3R7 
Go to UniProtKB:  A0A1C7A3R7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7A3R7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis.C [auth c]108Haloarcula californiae ATCC 33799Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis.D [auth d]75Haloarcula californiae ATCC 33799Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
(Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis.E [auth e]46Haloarcula californiae ATCC 33799Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Peripentonal unknown polypeptideF [auth f]18Haloarcula californiae ATCC 33799Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
VP4232Haloarcula californiae ATCC 33799Mutation(s): 0 
UniProt
Find proteins for A0A1C7A3R2 (Haloarcula californiae icosahedral virus 1)
Explore A0A1C7A3R2 
Go to UniProtKB:  A0A1C7A3R2
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UniProt GroupA0A1C7A3R2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTCoot0.8.8
MODEL REFINEMENTRosettaEM3.8
MODEL REFINEMENTPHENIX1.13-2988

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2015-64541-R
Spanish Ministry of Economy and CompetitivenessSpainSEV-2016-0644
Academy of FinlandFinland1306833, 255342,256518,283072
Other governmentSpainBasque Governament PRE_2016_2_0151

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Data processing
  • Version 1.2: 2022-12-14
    Changes: Database references, Derived calculations