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 1.2 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 1
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, y
157Homo sapiensMutation(s): 0 
Gene Names: ICAP1Integrin cytoplasmic domain-associated protein 1 (ICAP1)ITGB1BP1
Find proteins for O14713 (Homo sapiens)
Go to UniProtKB:  O14713
NIH Common Fund Data Resources
PHAROS  O14713
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-1
6, 7, 8, 9, B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, f, h, j, l, n, p, r, t, v, x, z
15Homo sapiensMutation(s): 0 
Gene Names: ITGB1FNRBMDF2MSK12
Find proteins for P05556 (Homo sapiens)
Go to UniProtKB:  P05556
NIH Common Fund Data Resources
PHAROS  P05556
Protein Feature View
  • 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