1JV2

CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN ALPHAVBETA3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of the extracellular segment of integrin alpha Vbeta3.

Xiong, J.P., Stehle, T., Diefenbach, B., Zhang, R., Dunker, R., Scott, D.L., Joachimiak, A., Goodman, S.L., Arnaout, M.A.

(2001) Science 294: 339-345

  • DOI: 10.1126/science.1064535

  • PubMed Abstract: 

    • Integrins are alphabeta heterodimeric receptors that mediate divalent cation-dependent cell-cell and cell-matrix adhesion through tightly regulated interactions with ligands. We have solved the crystal structure of the extracellular portion of integr ...

    Integrins are alphabeta heterodimeric receptors that mediate divalent cation-dependent cell-cell and cell-matrix adhesion through tightly regulated interactions with ligands. We have solved the crystal structure of the extracellular portion of integrin alphaVbeta3 at 3.1 A resolution. Its 12 domains assemble into an ovoid "head" and two "tails." In the crystal, alphaVbeta3 is severely bent at a defined region in its tails, reflecting an unusual flexibility that may be linked to integrin regulation. The main inter-subunit interface lies within the head, between a seven-bladed beta-propeller from alphaV and an A domain from beta3, and bears a striking resemblance to the Galpha/Gbeta interface in G proteins. A metal ion-dependent adhesion site (MIDAS) in the betaA domain is positioned to participate in a ligand-binding interface formed of loops from the propeller and betaA domains. MIDAS lies adjacent to a calcium-binding site with a potential regulatory function.

    Organizational Affiliation: 

    Renal Unit, Leukocyte Biology & Inflammation Program, Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTEGRIN, ALPHA V
A
957Homo sapiensMutation(s): 0 
Gene Names: ITGAV (MSK8, VNRA, VTNR)
Find proteins for P06756 (Homo sapiens)
Go to Gene View: ITGAV
Go to UniProtKB:  P06756
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PLATELET MEMBRANE GLYCOPROTEIN IIIA BETA SUBUNIT
B
692Homo sapiensMutation(s): 0 
Gene Names: ITGB3 (GP3A)
Find proteins for P05106 (Homo sapiens)
Go to Gene View: ITGB3
Go to UniProtKB:  P05106
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG
Download SDF File 
Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.255 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.000α = 90.00
b = 130.000β = 90.00
c = 307.300γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SHARPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance