1MQ8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.280 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1016/s0092-8674(02)01257-6
  • Structures With Same Primary Citation

  • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
intercellular adhesion molecule-1A, C291Homo sapiensMutation(s): 0 
Gene Names: ICAM-1ICAM1
Find proteins for P05362 (Homo sapiens)
Explore P05362 
Go to UniProtKB:  P05362
NIH Common Fund Data Resources
PHAROS  P05362
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-LB, D177Homo sapiensMutation(s): 2 
Gene Names: LFA-1 (AlphaLbeta2)ITGALCD11A
Find proteins for P20701 (Homo sapiens)
Explore P20701 
Go to UniProtKB:  P20701
NIH Common Fund Data Resources
PHAROS  P20701
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.280 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.56α = 95.39
b = 62.868β = 106.67
c = 81.517γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary