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 

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
  • Primary Citation of Related Structures:  

  • 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 1
A, 0, k, m, 1, C, 2, E, 3, G, o, q, I, 4, K, 5, M, O, a, s, u, c, e, g, i, Q, S, U, W, w, Y, y
157Homo sapiensMutation(s): 0 
Gene Names: ITGB1BP1 (ICAP1)
Find proteins for O14713 (Homo sapiens)
Go to Gene View: ITGB1BP1
Go to UniProtKB:  O14713
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-1
l, n, x, D, 8, H, p, B, 9, F, r, J, 7, L, 6, N, P, t, v, b, d, f, h, j, R, T, V, X, Z, z
15Homo sapiensMutation(s): 0 
Gene Names: ITGB1 (FNRB, MDF2, MSK12)
Find proteins for P05556 (Homo sapiens)
Go to Gene View: ITGB1
Go to UniProtKB:  P05556
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
0, 1, 2, 3, 4, 5, a, A, c, C, e, E, G, g, i, I, k, K, m, M, O, o, Q, q, s, S, u, U, W, w, y, Y
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 
  • 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
PDB_EXTRACTdata extraction
CBASSdata collection
REFMACrefinement
HKL-2000data reduction
AutoSolphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references
  • Version 1.2: 2013-03-13
    Type: Database references