3K72

Structure of integrin alphaX beta2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.315 
  • R-Value Observed: 0.315 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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-XA, C1095Homo sapiensMutation(s): 0 
Gene Names: CD11CITGAX
Find proteins for P20702 (Homo sapiens)
Explore P20702 
Go to UniProtKB:  P20702
NIH Common Fund Data Resources
PHAROS  P20702
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-2B, D687Homo sapiensMutation(s): 0 
Gene Names: CD18ITGB2MFI7
Find proteins for P05107 (Homo sapiens)
Explore P05107 
Go to UniProtKB:  P05107
NIH Common Fund Data Resources
PHAROS  P05107
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, I
2 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, J
5 N-Glycosylation
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, K
3 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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A, B, C, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
C
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.315 
  • R-Value Observed: 0.315 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.962α = 90
b = 165.549β = 90
c = 536.178γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SOLVEphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary