Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.39 kDa 
• Atom Count: 1757 
• Modelled Residue Count: 179 
• Deposited Residue Count: 179 
• Unique protein chains: 1

1MJN

Crystal Structure of the intermediate affinity aL I domain mutant

• PDB DOI: 10.2210/pdb1MJN/pdb

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


• Deposited: 2002-08-28 Released: 2003-01-28 
• Deposition Author(s): Shimaoka, M., Xiao, T., Liu, J.H., Yang, Y.T., Dong, Y.C., Jun, C.D., McCormack, A., Zhang, R.G., Wang, J.H., Springer, T.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.202 
• R-Value Work: 0.156 

Literature

Structures of the alphaL 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.T., Dong, Y.C., Jun, C.D., McCormack, A., Zhang, R.G., 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:  
  1MJN, 1MQ8, 1MQ9, 1MQA


• 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.

---

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
Integrin alpha-L	A	179	Homo sapiens	Mutation(s): 2  Gene Names: ITGAL, CD11A
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens) Explore P20701  Go to UniProtKB:  P20701
PHAROS:  P20701

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.202 
• R-Value Work: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.374	α = 90
b = 57.399	β = 90
c = 66.909	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-08-28 
• Released Date: 2003-01-28 
Deposition Author(s): Shimaoka, M., Xiao, T., Liu, J.H., Yang, Y.T., Dong, Y.C., Jun, C.D., McCormack, A., Zhang, R.G., Wang, J.H., Springer, T.A.

Revision History  

• Version 1.0: 2003-01-28
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations