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 by antagonizing ICAP1 (Integrin Cytoplasmic Associated Protein-1)-mediated modulation of "inside-out" 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-1-binding protein 1157Homo sapiensMutation(s): 0 
Gene Names: ICAP1, Integrin 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
PHAROS:  O14713
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14713
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-115Homo sapiensMutation(s): 0 
Gene Names: ITGB1, FNRB, MDF2, MSK12
UniProt & NIH Common Fund Data Resources
Find proteins for P05556 (Homo sapiens)
Explore P05556 
Go to UniProtKB:  P05556
PHAROS:  P05556
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05556
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,
B [auth 0],
BA [auth K],
BB [auth U],
C [auth k],
A,
B [auth 0],
BA [auth K],
BB [auth U],
C [auth k],
CA [auth 5],
DB [auth W],
E [auth m],
EB [auth w],
FA [auth M],
G [auth 1],
GB [auth Y],
H [auth C],
HA [auth O],
HB [auth y],
JA [auth a],
K [auth 2],
KA [auth s],
L [auth E],
M [auth 3],
MA [auth u],
N [auth G],
PA [auth c],
Q [auth o],
RA [auth e],
S [auth q],
TA [auth g],
VA [auth i],
X [auth I],
XA [auth Q],
Y [auth 4],
ZA [auth S]
L-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
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

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View more in-depth experimental data
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