› 6h9c

Electron Microscopy
3.74Å resolution

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

Released:
DOI: 10.2210/pdb6h9c/pdb
PDB entry 6h9c coloured by chain, front view.
PDB entry 6h9c coloured by chain, side view.
PDB entry 6h9c coloured by chain, top view.
Source organism: Haloarcula californiae ATCC 33799
Primary publication:
Structural basis for assembly of vertical single β-barrel viruses.
Santos-Pérez I, Charro D, Gil-Carton D, Azkargorta M, Elortza F, Bamford DH, Oksanen HM, Abrescia NGA
OpenAccess logo Nat Commun 10 1184 (2019)
PMID: 30862777
Related structures: EMD-0174

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 1920-mer (preferred)
PDBe Complex ID:
PDB-CPX-103310 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
VP7 Chains: D, E, F, I, J, K, L, M, N, R, S, T, W, Y, a
Molecule details ›
Chains: D, E, F, I, J, K, L, M, N, R, S, T, W, Y, a
Length: 184 amino acids
Theoretical weight: 19.91 KDa
Source organism: Haloarcula californiae ATCC 33799
UniProt:
  • Canonical: A0A1C7A3R1 (Residues: 1-184; Coverage: 100%)
Gene name: SS136_020
VP9 Chain: b
Molecule details ›
Chain: b
Length: 146 amino acids
Theoretical weight: 16.27 KDa
Source organism: Haloarcula californiae ATCC 33799
UniProt:
  • Canonical: A0A1C7A3R7 (Residues: 1-146; Coverage: 100%)
Gene name: SS136_027
GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis. Chain: c
Molecule details ›
Chain: c
Length: 108 amino acids
Theoretical weight: 9.21 KDa
Source organism: Haloarcula californiae ATCC 33799
GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis. Chain: d
Molecule details ›
Chain: d
Length: 75 amino acids
Theoretical weight: 6.4 KDa
Source organism: Haloarcula californiae ATCC 33799
(Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis. Chain: e
Molecule details ›
Chain: e
Length: 46 amino acids
Theoretical weight: 3.93 KDa
Source organism: Haloarcula californiae ATCC 33799
Peripentonal unknown polypeptide Chain: f
Molecule details ›
Chain: f
Length: 18 amino acids
Theoretical weight: 1.55 KDa
Source organism: Haloarcula californiae ATCC 33799
VP4 Chains: A, B, C, G, H, O, P, Q, U, V, X, Z
Molecule details ›
Chains: A, B, C, G, H, O, P, Q, U, V, X, Z
Length: 232 amino acids
Theoretical weight: 26 KDa
Source organism: Haloarcula californiae ATCC 33799
UniProt:
  • Canonical: A0A1C7A3R2 (Residues: 1-232; Coverage: 100%)
Gene name: SS136_021

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.74Å
Relevant EMDB volumes: EMD-0174

Quick links

Citations

8 review citations

Global Organization and Proposed Megataxonomy of the Virus World.
Koonin et al. (2020)
7 more

2 mentions without citation

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires.
Schoelmerich et al. (2024)
1 more