1U8C

A novel adaptation of the integrin PSI domain revealed from its crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.293 

wwPDB Validation 3D Report Full Report



Literature

A novel adaptation of the integrin PSI domain revealed from its crystal structure.

Xiong, J.P.Stehle, T.Goodman, S.L.Arnaout, M.A.

(2004) J Biol Chem 279: 40252-40254

  • DOI: 10.1074/jbc.C400362200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Integrin beta-subunits contain an N-terminal PSI (for plexin-semaphorin-integrin) domain that contributes to integrin activation and harbors the PI(A) alloantigen associated with immune thrombocytopenias and susceptibility to sudden cardiac death. He ...

    Integrin beta-subunits contain an N-terminal PSI (for plexin-semaphorin-integrin) domain that contributes to integrin activation and harbors the PI(A) alloantigen associated with immune thrombocytopenias and susceptibility to sudden cardiac death. Here we report the crystal structure of PSI in the context of the crystallized alphaVbeta3 ectodomain. The integrin PSI forms a two-stranded antiparallel beta-sheet flanked by two short helices; its long interstrand loop houses Pl(A) and may face the EGF2 domain. The integrin PSI contains four cysteine pairs connected in a 1-4, 2-8, 3-6, 5-7 pattern. An unexpected feature of the structure is that the final, eighth cysteine is located C-terminal to the Ig-like hybrid domain and is thus separated by the hybrid domain from the other seven cysteines of PSI. This architecture may be relevant to the evolution of integrins and should help refine the current models of integrin activation.


    Organizational Affiliation

    Structural Biology Program, Leukocyte Biology and Inflammation Program, Renal Unit.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-VA957Homo sapiensMutation(s): 0 
Gene Names: ITGAVVNRAMSK8VTNR
Find proteins for P06756 (Homo sapiens)
Explore P06756 
Go to UniProtKB:  P06756
NIH Common Fund Data Resources
PHAROS  P06756
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-3B692Homo sapiensMutation(s): 0 
Gene Names: ITGB3GP3A
Find proteins for P05106 (Homo sapiens)
Explore P05106 
Go to UniProtKB:  P05106
NIH Common Fund Data Resources
PHAROS  P05106
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
C, D, E, G
2 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, I
2 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.293 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130α = 90
b = 130β = 90
c = 307.3γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary