3K71

Structure of integrin alphaX beta2 ectodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.373 
  • R-Value Work: 0.350 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of an integrin with an alphaI domain, complement receptor type 4.

Xie, C.Zhu, J.Chen, X.Mi, L.Nishida, N.Springer, T.A.

(2010) Embo J. 29: 666-679

  • DOI: 10.1038/emboj.2009.367
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the structure of an integrin with an alphaI domain, alpha(X)beta(2), the complement receptor type 4. It was earlier expected that a fixed orientation between the alphaI domain and the beta-propeller domain in which it is inserted would be r ...

    We report the structure of an integrin with an alphaI domain, alpha(X)beta(2), the complement receptor type 4. It was earlier expected that a fixed orientation between the alphaI domain and the beta-propeller domain in which it is inserted would be required for allosteric signal transmission. However, the alphaI domain is highly flexible, enabling two betaI domain conformational states to couple to three alphaI domain states, and greater accessibility for ligand recognition. Although alpha(X)beta(2) is bent similarly to integrins that lack alphaI domains, the terminal domains of the alpha- and beta-legs, calf-2 and beta-tail, are oriented differently than in alphaI-less integrins. Linkers extending to the transmembrane domains are unstructured. Previous mutations in the beta(2)-tail domain support the importance of extension, rather than a deadbolt, in integrin activation. The locations of further activating mutations and antibody epitopes show the critical role of extension, and conversion from the closed to the open headpiece conformation, in integrin activation. Differences among 10 molecules in crystal lattices provide unprecedented information on interdomain flexibility important for modelling integrin extension and activation.


    Organizational Affiliation

    Department of Pathology, Harvard Medical School, Immune Disease Institute and Children's Hospital, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-X
A, C, E, G
1095Homo sapiensMutation(s): 0 
Gene Names: ITGAX (CD11C)
Find proteins for P20702 (Homo sapiens)
Go to Gene View: ITGAX
Go to UniProtKB:  P20702
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-2
B, D, F, H
687Homo sapiensMutation(s): 0 
Gene Names: ITGB2 (CD18, MFI7)
Find proteins for P05107 (Homo sapiens)
Go to Gene View: ITGB2
Go to UniProtKB:  P05107
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, C, E, G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
MG
Query on MG

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.373 
  • R-Value Work: 0.350 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 149.664α = 90.00
b = 165.745β = 90.00
c = 537.676γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
XDSdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance