6H82 | pdb_00006h82

Cryo-EM structure of the archaeal extremophilic internal membrane containing Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.78 Angstroms resolution.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 636.57 kDa 
  • Atom Count: 44,308 
  • Modeled Residue Count: 5,906 
  • Deposited Residue Count: 5,906 
  • Unique protein chains: 8

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VP4229Haloarcula hispanica icosahedral virus 2Mutation(s): 0 
UniProt
Find proteins for H9AZX2 (Haloarcula hispanica icosahedral virus 2)
Explore H9AZX2 
Go to UniProtKB:  H9AZX2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9AZX2
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
VP7B [auth D],
H [auth T],
N [auth J],
R [auth W]
172Haloarcula hispanica icosahedral virus 2Mutation(s): 0 
UniProt
Find proteins for H9AZX1 (Haloarcula hispanica icosahedral virus 2)
Explore H9AZX1 
Go to UniProtKB:  H9AZX1
Entity Groups
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UniProt GroupH9AZX1
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VP7175Haloarcula hispanica icosahedral virus 2Mutation(s): 0 
UniProt
Find proteins for H9AZX1 (Haloarcula hispanica icosahedral virus 2)
Explore H9AZX1 
Go to UniProtKB:  H9AZX1
Entity Groups
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UniProt GroupH9AZX1
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
VP7AA [auth Y],
W [auth L],
X [auth I]
161Haloarcula hispanica icosahedral virus 2Mutation(s): 0 
UniProt
Find proteins for H9AZX1 (Haloarcula hispanica icosahedral virus 2)
Explore H9AZX1 
Go to UniProtKB:  H9AZX1
Entity Groups
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UniProt GroupH9AZX1
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized proteinBA [auth b]135Haloarcula hispanica icosahedral virus 2Mutation(s): 0 
UniProt
Find proteins for H9AZX8 (Haloarcula hispanica icosahedral virus 2)
Explore H9AZX8 
Go to UniProtKB:  H9AZX8
Entity Groups
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UniProt GroupH9AZX8
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
VP16 (vertex complex)CA [auth g]217Haloarcula hispanica icosahedral virus 2Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
GPS IIIDA [auth c],
EA [auth d]
105Haloarcula hispanica icosahedral virus 2Mutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
polypeptide stretch (vertex complex)FA [auth m]25Haloarcula hispanica icosahedral virus 2Mutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

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_151)

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Data collection, Other
  • Version 1.2: 2020-06-17
    Changes: Refinement description
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Derived calculations