3FCU

Structure of headpiece of integrin aIIBb3 in open conformation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure of a complete integrin ectodomain in a physiologic resting state and activation and deactivation by applied forces.

Zhu, J., Luo, B.H., Xiao, T., Zhang, C., Nishida, N., Springer, T.A.

(2008) Mol.Cell 32: 849-861

  • DOI: 10.1016/j.molcel.2008.11.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The complete ectodomain of integrin alpha(IIb)beta(3) reveals a bent, closed, low-affinity conformation, the beta knee, and a mechanism for linking cytoskeleton attachment to high affinity for ligand. Ca and Mg ions in the recognition site, including ...

    The complete ectodomain of integrin alpha(IIb)beta(3) reveals a bent, closed, low-affinity conformation, the beta knee, and a mechanism for linking cytoskeleton attachment to high affinity for ligand. Ca and Mg ions in the recognition site, including the synergistic metal ion binding site (SyMBS), are loaded prior to ligand binding. Electrophilicity of the ligand-binding Mg ion is increased in the open conformation. The beta(3) knee passes between the beta(3)-PSI and alpha(IIb)-knob to bury the lower beta leg in a cleft, from which it is released for extension. Different integrin molecules in crystals and EM reveal breathing that appears on pathway to extension. Tensile force applied to the extended ligand-receptor complex stabilizes the closed, low-affinity conformation. By contrast, an additional lateral force applied to the beta subunit to mimic attachment to moving actin filaments stabilizes the open, high-affinity conformation. This mechanism propagates allostery over long distances and couples cytoskeleton attachment of integrins to their high-affinity state.

    Organizational Affiliation: 

    The Immune Disease Institute and Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin, alpha 2b
A, C, E
457Homo sapiensMutation(s): 0 
Gene Names: ITGA2B (GP2B, ITGAB)
Find proteins for P08514 (Homo sapiens)
Go to Gene View: ITGA2B
Go to UniProtKB:  P08514
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-3
B, D, F
461Homo 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A, B, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN
Download SDF File 
Download CCD File 
B, D, F
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC
Download SDF File 
Download CCD File 
B, D, F
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 332.093α = 90.00
b = 332.093β = 90.00
c = 88.288γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance