1MQ8

Crystal structure of alphaL I domain in complex with ICAM-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of the aL I domain and its complex with ICAM-1 reveal a shape-shifting pathway for integrin regulation

Shimaoka, M.Xiao, T.Liu, J.-H.Yang, Y.Dong, Y.Jun, C.-D.McCormack, A.Zhang, R.Joachimiak, A.Takagi, J.Wang, J.-H.Springer, T.A.

(2003) Cell 112: 99-111

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the I domain of integrin alpha L beta 2 bound to the Ig superfamily ligand ICAM-1 reveals the open ligand binding conformation and the first example of an integrin-IgSF interface. The I domain Mg2+ directly coordinates Glu-34 of ICAM ...

    The structure of the I domain of integrin alpha L beta 2 bound to the Ig superfamily ligand ICAM-1 reveals the open ligand binding conformation and the first example of an integrin-IgSF interface. The I domain Mg2+ directly coordinates Glu-34 of ICAM-1, and a dramatic swing of I domain residue Glu-241 enables a critical salt bridge. Liganded and unliganded structures for both high- and intermediate-affinity mutant I domains reveal that ligand binding can induce conformational change in the alpha L I domain and that allosteric signals can convert the closed conformation to intermediate or open conformations without ligand binding. Pulling down on the C-terminal alpha 7 helix with introduced disulfide bonds ratchets the beta 6-alpha 7 loop into three different positions in the closed, intermediate, and open conformations, with a progressive increase in affinity.


    Organizational Affiliation

    The Center for Blood Research, Department of Pathology, Department of Anesthesia, Department of Pediatrics, Boston, Massachusetts 02115.,Dana-Farber Cancer Institute, Department of Pediatrics, Department of Medicine, Department of Biological Chemistry, Department of Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.,Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
intercellular adhesion molecule-1
A, C
291Homo sapiensMutation(s): 0 
Gene Names: ICAM1
Find proteins for P05362 (Homo sapiens)
Go to Gene View: ICAM1
Go to UniProtKB:  P05362
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-L
B, D
177Homo sapiensMutation(s): 2 
Gene Names: ITGAL (CD11A)
Find proteins for P20701 (Homo sapiens)
Go to Gene View: ITGAL
Go to UniProtKB:  P20701
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.264 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.560α = 95.39
b = 62.868β = 106.67
c = 81.517γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
HKL-2000data collection
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance