5KHO

Rasip1 RA domain in complex with Rap1B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Dimeric Rasip1 RA Domain Recognition of the Ras Subfamily of GTP-Binding Proteins.

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

(2016) Structure 24: 2152-2162

  • DOI: 10.1016/j.str.2016.10.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ras-interacting protein 1 (Rasip1) is an endothelial-specific Rap1 and Ras effector, important for vascular development and angiogenesis. Here, we report the crystal structure of the Rasip1 RA domain (RRA) alone, revealing the basis of dimerization, ...

    Ras-interacting protein 1 (Rasip1) is an endothelial-specific Rap1 and Ras effector, important for vascular development and angiogenesis. Here, we report the crystal structure of the Rasip1 RA domain (RRA) alone, revealing the basis of dimerization, and in complex with Rap1 at 2.8 Å resolution. In contrast to most RA domains, RRA formed a dimer that can bind two Rap1 (K D  = 0.9 μM) or Ras (K D  = 2.2 μM) molecules. We solved the Rap1-RRA complex and found that Rasip1 binds Rap1 in the Switch I region, and Rap1 binding induces few conformation changes to Rasip1 stabilizing a β strand and an unstructured loop. Our data explain how Rasip1 can act as a Rap1 and Ras effector and show that Rasip1 defines a subgroup of dimeric RA domains that could mediate cooperative binding to membrane-associated Ras superfamily members.


    Organizational Affiliation

    Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address: agingras@ucsd.edu.,Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-interacting protein 1
A, B
156Homo sapiensMutation(s): 0 
Gene Names: RASIP1
Find proteins for Q5U651 (Homo sapiens)
Go to Gene View: RASIP1
Go to UniProtKB:  Q5U651
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rap-1b
C, D
167Homo sapiensMutation(s): 0 
Gene Names: RAP1B
Find proteins for P61224 (Homo sapiens)
Go to Gene View: RAP1B
Go to UniProtKB:  P61224
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
C, D
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.540α = 90.00
b = 154.760β = 90.00
c = 38.800γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-06-15 
  • Released Date: 2016-10-19 
  • Deposition Author(s): Gingras, A.R.

Funding OrganizationLocationGrant Number
American Heart AssociationUnited States12SDG11610043
American Heart AssociationUnited States16GRNT29650005

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-02-15
    Type: Database references
  • Version 1.2: 2017-10-04
    Type: Author supporting evidence