› 5ner

Electron Microscopy
11.5Å resolution

Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O PanAsia - Pose A prime.

Released:
DOI: 10.2210/pdb5ner/pdb
PDB entry 5ner coloured by chain, front view.
PDB entry 5ner coloured by chain, side view.
PDB entry 5ner coloured by chain, top view.
Source organisms:
Primary publication:
Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus.
Kotecha A, Wang Q, Dong X, Ilca SL, Ondiviela M, Zihe R, Seago J, Charleston B, Fry EE, Abrescia NGA, Springer TA, Huiskonen JT, Stuart DI
Nat Commun 8 15408 (2017)
PMID: 28534487
Related structures: EMD-3633

Function and Biology Details

Reactions catalysed: 
Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-.
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108159 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (11 distinct):
Viral protein 1 (VP1) Chain: 1
Molecule details ›
Chain: 1
Length: 210 amino acids
Theoretical weight: 23.27 KDa
Source organism: Foot-and-mouth disease virus
Expression system: Cricetinae gen. sp.
UniProt:
  • Canonical: Q98W00 (Residues: 1-210; Coverage: 99%)
Gene name: 1D
Sequence domains: picornavirus capsid protein
O PanAsia VP2 Chain: 2
Molecule details ›
Chain: 2
Length: 214 amino acids
Theoretical weight: 23.91 KDa
Source organism: Foot-and-mouth disease virus
Expression system: Cricetinae gen. sp.
UniProt:
  • Canonical: Q6ZZ87 (Residues: 291-504; Coverage: 9%)
Gene name: polyprotein
Sequence domains: picornavirus capsid protein
O PanAsia VP3 Chain: 3
Molecule details ›
Chain: 3
Length: 220 amino acids
Theoretical weight: 23.94 KDa
Source organism: Foot-and-mouth disease virus
Expression system: Cricetinae gen. sp.
UniProt:
  • Canonical: Q6ZZ87 (Residues: 505-724; Coverage: 9%)
Gene name: polyprotein
Sequence domains: picornavirus capsid protein
O PanAsia VP4 Chain: 4
Molecule details ›
Chain: 4
Length: 70 amino acids
Theoretical weight: 7.52 KDa
Source organism: Foot-and-mouth disease virus
Expression system: Cricetinae gen. sp.
UniProt:
  • Canonical: A6Y878 (Residues: 218-287; Coverage: 3%)
Sequence domains: Viral protein VP4 subunit
Integrin alpha-V heavy chain Chain: A
Molecule details ›
Chain: A
Length: 594 amino acids
Theoretical weight: 65.35 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P06756 (Residues: 31-624; Coverage: 58%)
Gene names: ITGAV, MSK8, VNRA, VTNR
Sequence domains:
Integrin beta-6 Chain: B
Molecule details ›
Chain: B
Length: 470 amino acids
Theoretical weight: 51.53 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P18564 (Residues: 22-491; Coverage: 61%)
Gene name: ITGB6
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: MAN, NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: MAN, NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: MAN, NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: MAN, NAG
Carbohydrate polymer
3 bound ligands:
Ligand MAN 3 x MAN
Ligand NAG 4 x NAG
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 11.5Å
Relevant EMDB volumes: EMD-3633
Expression systems:
  • Cricetinae gen. sp.
  • Homo sapiens

Quick links

Citations

14 review citations

Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein.
Makowski et al. (2021)
13 more

2 mentions without citation

Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus.
Kotecha et al. (2017)
1 more