4HDO

Crystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The Structure of the Ternary Complex of Krev Interaction Trapped 1 (KRIT1) Bound to Both the Rap1 GTPase and the Heart of Glass (HEG1) Cytoplasmic Tail.

Gingras, A.R., Puzon-McLaughlin, W., Ginsberg, M.H.

(2013) J Biol Chem 288: 23639-23649

  • DOI: 10.1074/jbc.M113.462911
  • Primary Citation of Related Structures:  
    4HDO, 4HDQ

  • PubMed Abstract: 

    • Loss of function mutation in Krev interaction trapped 1 (KRIT1) causes autosomal dominant familial cerebral cavernous malformations and disrupts cardiovascular development. The biological function of KRIT1 requires that its FERM (band 4.1, ezrin, radixin ...

    Loss of function mutation in Krev interaction trapped 1 (KRIT1) causes autosomal dominant familial cerebral cavernous malformations and disrupts cardiovascular development. The biological function of KRIT1 requires that its FERM (band 4.1, ezrin, radixin, moesin) domain physically interact with both the small GTPase Rap1 and the cytoplasmic tail of the Heart of glass (HEG1) membrane anchor. In this study, we show that the KRIT1 FERM domain can bind both Rap1 and HEG1 simultaneously, and we solved the crystal structure of the KRIT1-Rap1-HEG1 ternary complex. Rap1 binds on the surface of the F1 and F2 subdomains, in an interaction that leaves its Switch II region accessible to other potential effectors. HEG1 binds in a hydrophobic pocket at the KRIT1 F1 and F3 interface, and there is no overlap with the Rap1-binding site. Indeed, the affinity of KRIT1 or the KRIT1-Rap1 complex for HEG1 is comparable (Kd = 1.2 and 0.96 μm, respectively) showing that there is no competition between the two sites. Furthermore, analysis of this structure revealed a specific ionic interaction between the F2 lobe of KRIT1 and Rap1 that could explain the remarkable Rap1 specificity of KRIT1. This structural insight enabled design of KRIT1(K570I), a mutant that binds Rap1 with 8-fold lower affinity and exhibits increased binding to HRas. These data show that HEG1 can recruit the Rap1-KRIT complex to the plasma membrane where Rap1's Switch II region remains accessible and reveals an important determinant of KRIT1's specificity for Rap1.

    Organizational Affiliation: 

    Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA. agingras@ucsd.edu



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Krev interaction trapped protein 1 A322Homo sapiensMutation(s): 0 
Gene Names: KRIT1, CCM1
Find proteins for O00522 (Homo sapiens)
Explore O00522 
Go to UniProtKB:  O00522
NIH Common Fund Data Resources
PHAROS:  O00522
GTEx:  ENSG00000001631
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rap-1b B167Homo sapiensMutation(s): 0 
Gene Names: RAP1B, OK/SW-cl.11
EC: 3.6.5.2
Find proteins for P61224 (Homo sapiens)
Explore P61224 
Go to UniProtKB:  P61224
NIH Common Fund Data Resources
PHAROS:  P61224
GTEx:  ENSG00000127314
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
B
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.85α = 90
b = 77.75β = 91.2
c = 58.85γ = 90
Software Package:
Software NamePurpose
dlsdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-10-02 
  • Released Date: 2013-07-10 
    • Deposition Author(s): Gingras, A.R.

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-09-04
    Changes: Database references