6AXF

Structure of RasGRP2 in complex with Rap1B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A histidine pH sensor regulates activation of the Ras-specific guanine nucleotide exchange factor RasGRP1.

Vercoulen, Y.Kondo, Y.Iwig, J.S.Janssen, A.White, K.A.Amini, M.Barber, D.L.Kuriyan, J.Roose, J.P.

(2017) Elife 6

  • DOI: 10.7554/eLife.29002
  • Primary Citation of Related Structures:  
    6AXF, 6AXG

  • PubMed Abstract: 
  • RasGRPs are guanine nucleotide exchange factors that are specific for Ras or Rap, and are important regulators of cellular signaling. Aberrant expression or mutation of RasGRPs results in disease. An analysis of RasGRP1 SNP variants led to the conclusion that the charge of His 212 in RasGRP1 alters signaling activity and plasma membrane recruitment, indicating that His 212 is a pH sensor that alters the balance between the inactive and active forms of RasGRP1 ...

    RasGRPs are guanine nucleotide exchange factors that are specific for Ras or Rap, and are important regulators of cellular signaling. Aberrant expression or mutation of RasGRPs results in disease. An analysis of RasGRP1 SNP variants led to the conclusion that the charge of His 212 in RasGRP1 alters signaling activity and plasma membrane recruitment, indicating that His 212 is a pH sensor that alters the balance between the inactive and active forms of RasGRP1. To understand the structural basis for this effect we compared the structure of autoinhibited RasGRP1, determined previously, to those of active RasGRP4:H-Ras and RasGRP2:Rap1b complexes. The transition from the autoinhibited to the active form of RasGRP1 involves the rearrangement of an inter-domain linker that displaces inhibitory inter-domain interactions. His 212 is located at the fulcrum of these conformational changes, and structural features in its vicinity are consistent with its function as a pH-dependent switch.


    Organizational Affiliation

    Department of Anatomy, University of California, San Francisco, San Francisco, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAS guanyl-releasing protein 2A, C, E, G, I, K, M, O397Homo sapiensMutation(s): 0 
Gene Names: RASGRP2CDC25LMCG7
UniProt & NIH Common Fund Data Resources
Find proteins for Q7LDG7 (Homo sapiens)
Explore Q7LDG7 
Go to UniProtKB:  Q7LDG7
PHAROS:  Q7LDG7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rap-1bB, D, F, H, J, L, N, P169Homo sapiensMutation(s): 0 
Gene Names: RAP1BOK/SW-cl.11
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61224 (Homo sapiens)
Explore P61224 
Go to UniProtKB:  P61224
PHAROS:  P61224
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C, E, G, I, K, M, OL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.998α = 90
b = 209.258β = 90
c = 336.765γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release