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 1.4 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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin beta-1-binding protein 1A,
B,
C [auth D],
D [auth E]
154Homo sapiensMutation(s): 0 
Gene Names: ICAP1Integrin cytoplasmic domain-associated protein 1 (ICAP1)ITGB1BP1
UniProt & NIH Common Fund Data Resources
Find proteins for O14713 (Homo sapiens)
Explore O14713 
Go to UniProtKB:  O14713
GTEx:  ENSG00000119185 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14713
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Krev interaction trapped protein 1E [auth H],
F [auth I],
G [auth J],
H [auth K]
203Homo sapiensMutation(s): 0 
Gene Names: CCM1Krev interaction trapped protein 1 (KRIT1)KRIT1
UniProt & NIH Common Fund Data Resources
Find proteins for O00522 (Homo sapiens)
Explore O00522 
Go to UniProtKB:  O00522
GTEx:  ENSG00000001631 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00522
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth B]
M [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth D],
P [auth D],
Q [auth D],
R [auth D],
S [auth E],
T [auth E],
U [auth E],
V [auth H],
W [auth H],
X [auth H]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

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  (Full details and data files)

  • 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
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Refinement description