6OM2 image
Deposition Date 2019-04-17
Release Date 2019-12-11
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6OM2
Keywords:
Title:
Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.77 Å
R-Value Free:
0.28
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Integrin alpha-V
Gene (Uniprot):ITGAV
Mutations:M400GC
Chain IDs:A, C
Chain Length:598
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Integrin beta-8
Gene (Uniprot):ITGB8
Mutations:V259C
Chain IDs:B, D
Chain Length:421
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:proTGF-beta1 RGD peptide
Chain IDs:E, F
Chain Length:11
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
General structural features that regulate integrin affinity revealed by atypical alpha V beta 8.
Nat Commun 10 5481 5481 (2019)
PMID: 31792290 DOI: 10.1038/s41467-019-13248-5

Abstact

Integrin αVβ8, which like αVβ6 functions to activate TGF-βs, is atypical. Its β8 subunit binds to a distinctive cytoskeleton adaptor and does not exhibit large changes in conformation upon binding to ligand. Here, crystal structures, hydrogen-deuterium exchange dynamics, and affinity measurements on mutants are used to compare αVβ8 and αVβ6. Lack of a binding site for one of three βI domain divalent cations and a unique β6-α7 loop conformation in β8 facilitate movements of the α1 and α1' helices at the ligand binding pocket toward the high affinity state, without coupling to β6-α7 loop reshaping and α7-helix pistoning that drive large changes in βI domain-hybrid domain orientation seen in other integrins. Reciprocal swaps between β6 and β8 βI domains increase affinity of αVβ6 and decrease affinity of αVβ8 and define features that regulate affinity of the βI domain and its coupling to the hybrid domain.

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