3VI3
Crystal structure of alpha5beta1 integrin headpiece (ligand-free form)
Summary for 3VI3
| Entry DOI | 10.2210/pdb3vi3/pdb |
| Related | 3VI4 |
| Descriptor | Integrin alpha-5, Integrin beta-1, SG/19 Fab fragment (Light chain), ... (9 entities in total) |
| Functional Keywords | beta propeller fold, rossmann fold, beta sandwich, fibronectin receptor, cell adhesion-immune system complex, cell adhesion/immune system |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 8 |
| Total formula weight | 338847.41 |
| Authors | Nagae, M.,Nogi, T.,Takagi, J. (deposition date: 2011-09-21, release date: 2012-02-22, Last modification date: 2020-07-29) |
| Primary citation | Nagae, M.,Re, S.,Mihara, E.,Nogi, T.,Sugita, Y.,Takagi, J. Crystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor J.Cell Biol., 197:131-140, 2012 Cited by PubMed Abstract: Integrin α5β1 is a major cellular receptor for the extracellular matrix protein fibronectin and plays a fundamental role during mammalian development. A crystal structure of the α5β1 integrin headpiece fragment bound by an allosteric inhibitory antibody was determined at a 2.9-Å resolution both in the absence and presence of a ligand peptide containing the Arg-Gly-Asp (RGD) sequence. The antibody-bound β1 chain accommodated the RGD ligand with very limited structural changes, which may represent the initial step of cell adhesion mediated by nonactivated integrins. Furthermore, a molecular dynamics simulation pointed to an important role for Ca(2+) in the conformational coupling between the ligand-binding site and the rest of the molecule. The RGD-binding pocket is situated at the center of a trenchlike exposed surface on the top face of α5β1 devoid of glycosylation sites. The structure also enabled the precise prediction of the acceptor residue for the auxiliary synergy site of fibronectin on the α5 subunit, which was experimentally confirmed by mutagenesis and kinetic binding assays. PubMed: 22451694DOI: 10.1083/jcb.201111077 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.9 Å) |
Structure validation
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