4KVG

Crystal structure of RIAM RA-PH domains in complex with GTP bound Rap1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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This is version 1.2 of the entry. See complete history


Literature

The structure of Rap1 in complex with RIAM reveals specificity determinants and recruitment mechanism.

Zhang, H.Chang, Y.C.Brennan, M.L.Wu, J.

(2014) J Mol Cell Biol 6: 128-139

  • DOI: https://doi.org/10.1093/jmcb/mjt044
  • Primary Citation of Related Structures:  
    4KVG

  • PubMed Abstract: 

    The small GTPase Rap1 induces integrin activation via an inside-out signaling pathway mediated by the Rap1-interacting adaptor molecule (RIAM). Blocking this pathway may suppress tumor metastasis and other diseases that are related to hyperactive integrins. However, the molecular basis for the specific recognition of RIAM by Rap1 remains largely unknown. Herein we present the crystal structure of an active, GTP-bound GTPase domain of Rap1 in complex with the Ras association (RA)-pleckstrin homology (PH) structural module of RIAM at 1.65 Å. The structure reveals that the recognition of RIAM by Rap1 is governed by side-chain interactions. Several side chains are critical in determining specificity of this recognition, particularly the Lys31 residue in Rap1 that is oppositely charged compared with the Glu31/Asp31 residue in other Ras GTPases. Lys31 forms a salt bridge with RIAM residue Glu212, making it the key specificity determinant of the interaction. We also show that disruption of these interactions results in reduction of Rap1:RIAM association, leading to a loss of co-clustering and cell adhesion. Our findings elucidate the molecular mechanism by which RIAM mediates Rap1-induced integrin activation. The crystal structure also offers new insight into the structural basis for the specific recruitment of RA-PH module-containing effector proteins by their small GTPase partners.


  • Organizational Affiliation

    Developmental Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rap-1A
A, C
168Homo sapiensMutation(s): 2 
Gene Names: KREV1RAP1A
UniProt & NIH Common Fund Data Resources
Find proteins for P62834 (Homo sapiens)
Explore P62834 
Go to UniProtKB:  P62834
PHAROS:  P62834
GTEx:  ENSG00000116473 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62834
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
B, D
260Mus musculusMutation(s): 0 
Gene Names: Apbb1ipPrel1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8R5A3 (Mus musculus)
Explore Q8R5A3 
Go to UniProtKB:  Q8R5A3
IMPC:  MGI:1861354
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R5A3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.467α = 90
b = 85.848β = 90
c = 160.852γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations