› 6om2

X-ray diffraction
2.77Å resolution

Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide

Released:
DOI: 10.2210/pdb6om2/pdb
PDB entry 6om2 coloured by chain, front view.
PDB entry 6om2 coloured by chain, side view.
PDB entry 6om2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
General structural features that regulate integrin affinity revealed by atypical αVβ8.
Wang J, Su Y, Iacob RE, Engen JR, Springer TA
OpenAccess logo Nat Commun 10 5481 (2019)
PMID: 31792290

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-524805 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (9 distinct):
Integrin alpha-V heavy chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 598 amino acids
Theoretical weight: 65.63 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P06756 (Residues: 31-429, 430-624; Coverage: 58%)
Gene names: ITGAV, MSK8, VNRA, VTNR
Sequence domains:
Integrin beta-8 Chains: B, D
Molecule details ›
Chains: B, D
Length: 421 amino acids
Theoretical weight: 46.63 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P26012 (Residues: 43-463; Coverage: 58%)
Gene name: ITGB8
Sequence domains:
Latency-associated peptide Chains: E, F
Molecule details ›
Chains: E, F
Length: 11 amino acids
Theoretical weight: 1.16 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P01137 (Residues: 242-252; Coverage: 3%)
Gene names: TGFB, TGFB1

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
5 bound ligands:
Ligand CA 10 x CA
Ligand NAG 3 x NAG
Ligand PEG 2 x PEG
Ligand MG 2 x MG
Ligand GLY 1 x GLY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 161.19Å b: 53.85Å c: 176.62Å
α: 90° β: 111.47° γ: 90°
R-values:
R R work R free
0.252 0.251 0.282
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

2 review citations

αvβ8 integrin adhesion and signaling pathways in development, physiology and disease.
McCarty JH. (2020)
1 more

7 mentions without citation

Structural analysis of peptide binding to integrins for cancer detection and treatment.
Urquiza et al. (2023)
6 more