4DX8

ICAP1 in complex with KRIT1 N-terminus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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 activa ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-1-binding protein 1A, B, D, E154Homo 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 LengthOrganismDetails
Krev interaction trapped protein 1H, I, J, K203Homo sapiensMutation(s): 0 
Gene Names: CCM1Krev interaction trapped protein 1 (KRIT1)KRIT1
Find proteins for O00522 (Homo sapiens)
Explore O00522 
Go to UniProtKB:  O00522
NIH Common Fund Data Resources
PHAROS  O00522
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download CCD File 
A, B, D, E, H
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: C 2 2 21
  • Diffraction Data DOI: 10.15785/SBGRID/549 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.898α = 90
b = 157.977β = 90
c = 152.006γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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