4DX9

ICAP1 in complex with integrin beta 1 cytoplasmic tail


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism for KRIT1 Release of ICAP1-Mediated Suppression of Integrin Activation.

Liu, W.Draheim, K.M.Zhang, R.Calderwood, D.A.Boggon, T.J.

(2013) Mol Cell 49: 719-729

  • DOI: 10.1016/j.molcel.2012.12.005
  • Primary Citation of Related Structures:  
    4DX8, 4DX9

  • PubMed Abstract: 
  • KRIT1 (Krev/Rap1 Interaction Trapped-1) mutations are observed in ∼40% of autosomal-dominant cerebral cavernous malformations (CCMs), a disease occurring in up to 0.5% of the population. We show that KRIT1 functions as a switch for β1 integrin activation ...

    KRIT1 (Krev/Rap1 Interaction Trapped-1) mutations are observed in ∼40% of autosomal-dominant cerebral cavernous malformations (CCMs), a disease occurring in up to 0.5% of the population. We show that KRIT1 functions as a switch for β1 integrin activation by antagonizing ICAP1 (Integrin Cytoplasmic Associated Protein-1)-mediated modulation of "inside-out" activation. We present cocrystal structures of KRIT1 with ICAP1 and ICAP1 with integrin β1 cytoplasmic tail to 2.54 and 3.0 Å resolution (the resolutions at which I/σI = 2 are 2.75 and 3.0 Å, respectively). We find that KRIT1 binds ICAP1 by a bidentate surface, that KRIT1 directly competes with integrin β1 to bind ICAP1, and that KRIT1 antagonizes ICAP1-modulated integrin activation using this site. We also find that KRIT1 contains an N-terminal Nudix domain, in a region previously designated as unstructured. We therefore provide insights to integrin regulation and CCM-associated KRIT1 function.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-1-binding protein 1012345AC012345ACEGIKMOQSUWYacegikmoqsuwy
157Homo sapiensMutation(s): 0 
Gene Names: ICAP1Integrin cytoplasmic domain-associated protein 1 (ICAP1)ITGB1BP1
Find proteins for O14713 (Homo sapiens)
Explore O14713 
Go to UniProtKB:  O14713
NIH Common Fund Data Resources
PHAROS:  O14713
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-16789BDFH6789BDFHJLNPRTVXZbdfhjlnprtvxz
15Homo sapiensMutation(s): 0 
Gene Names: ITGB1FNRBMDF2MSK12
Find proteins for P05556 (Homo sapiens)
Explore P05556 
Go to UniProtKB:  P05556
NIH Common Fund Data Resources
PHAROS:  P05556
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
0,1,2,3,4,5,A,C,E,G,I,K,M,O,Q,S,U,W,Y,a,c,e,g,i,k,m,o,q,s,u,w,yL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.255 
  • Space Group: P 1
  • Diffraction Data DOI: 10.15785/SBGRID/550 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.622α = 89.97
b = 122.207β = 89.99
c = 135.269γ = 108.11
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references
  • Version 1.2: 2013-03-13
    Changes: Database references
  • Version 1.3: 2020-09-02
    Changes: Database references, Derived calculations, Structure summary