1N3Y | pdb_00001n3y

Crystal structure of the alpha-X beta2 integrin I domain

• PDB DOI: https://doi.org/10.2210/pdb1N3Y/pdb

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


• Deposited: 2002-10-30 Released: 2003-02-18 
• Deposition Author(s): Vorup-Jensen, T., Ostermeier, C., Shimaoka, M., Hommel, U., Springer, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: other

Literature

Structure and allosteric regulation of the alpha X beta 2 integrin I domain.

Vorup-Jensen, T., Ostermeier, C., Shimaoka, M., Hommel, U., Springer, T.A.

(2003) Proc Natl Acad Sci U S A 100: 1873-1878

• PubMed: 12554829 
• DOI: https://doi.org/10.1073/pnas.0237387100
• Primary Citation Related Structures: 
  1N3Y


• PubMed Abstract: 
  

  The integrin alpha X beta 2 (CD11c/CD18, p150,95) binds ligands through the I domain of the alpha X subunit. Ligands include the complement factor fragment iC3b, a key component in the innate immune defense, which, together with the expression of alpha X beta 2 on dendritic cells and on other leukocytes, suggests a role in the immune response. We now report the structure of the alpha X I domain resolved at 1.65 A by x-ray crystallography. To analyze structural requirements for ligand binding we made a mutation in the alpha X I domain C-terminal helix, which increased the affinity for iC3b approximately 200-fold to 2.4 microM compared with the wild-type domain affinity of approximately 400 microM. Gel permeation chromatography supported a conformational change between the wild-type and mutated domains. Conservation of allosteric regulation in the alpha X I domain points to the functional importance of this phenomenon.

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Organizational Affiliation: 
• Center for Blood Research, Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.36 kDa 
• Atom Count: 1,803 
• Modeled Residue Count: 189 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-X	A	198	Homo sapiens	Mutation(s): 2  Gene Names: ITGAX OR CD11C
UniProt & NIH Common Fund Data Resources
Find proteins for P20702 (Homo sapiens) Explore P20702  Go to UniProtKB:  P20702
PHAROS:  P20702 GTEx:  ENSG00000140678

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.694	α = 90
b = 84.694	β = 90
c = 65.776	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNX	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-18 
Deposition Author(s): Vorup-Jensen, T., Ostermeier, C., Shimaoka, M., Hommel, U., Springer, T.A.

Revision History  

• Version 1.0: 2003-02-18
  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
• Version 1.4: 2024-02-14
  Changes: Data collection
• Version 1.5: 2024-04-03
  Changes: Refinement description