Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.26 kDa 
• Atom Count: 5854 
• Residue Count: 722 
• Unique protein chains: 2

1MQ8

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

• DOI: 10.2210/pdb1MQ8/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-09-15 Released: 2003-01-14 
• Deposition Author(s): 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.

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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 

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

• PubMed: 12526797 
• DOI: 10.1016/s0092-8674(02)01257-6
• Primary Citation of Related Structures:  
  1MQ9, 1MQ8, 1MQA, 1MJN


• 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-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.

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Organizational Affiliation: 

The Center for Blood Research, Department of Pathology, Department of Anesthesia, Department of Pediatrics, Boston, Massachusetts 02115.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
intercellular adhesion molecule-1	A, C	291	Homo sapiens	Mutation(s): 0  Gene Names: ICAM-1, ICAM1
Find proteins for P05362 (Homo sapiens) Explore P05362  Go to UniProtKB:  P05362
NIH Common Fund Data Resources
PHAROS  P05362 GTEx  ENSG00000090339

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-L	B, D	177	Homo sapiens	Mutation(s): 2  Gene Names: LFA-1 (AlphaLbeta2), ITGAL, CD11A
Find proteins for P20701 (Homo sapiens) Explore P20701  Go to UniProtKB:  P20701
NIH Common Fund Data Resources
PHAROS  P20701 GTEx  ENSG00000005844

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D 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
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG	B, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 46.56	α = 95.39
b = 62.868	β = 106.67
c = 81.517	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-15 
• Released Date: 2003-01-14 
Deposition Author(s): 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.

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