4M8M

Crystal structure of the active dimer of zebrafish PlexinC1 cytoplasmic region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.307 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin.

Wang, Y.Pascoe, H.G.Brautigam, C.A.He, H.Zhang, X.

(2013) Elife 2: e01279-e01279

  • DOI: 10.7554/eLife.01279
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plexins are cell surface receptors that bind semaphorins and transduce signals for regulating neuronal axon guidance and other processes. Plexin signaling depends on their cytoplasmic GTPase activating protein (GAP) domain, which specifically inactiv ...

    Plexins are cell surface receptors that bind semaphorins and transduce signals for regulating neuronal axon guidance and other processes. Plexin signaling depends on their cytoplasmic GTPase activating protein (GAP) domain, which specifically inactivates the Ras homolog Rap through an ill-defined non-canonical catalytic mechanism. The plexin GAP is activated by semaphorin-induced dimerization, the structural basis for which remained unknown. Here we present the crystal structures of the active dimer of zebrafish PlexinC1 cytoplasmic region in the apo state and in complex with Rap. The structures show that the dimerization induces a large-scale conformational change in plexin, which opens the GAP active site to allow Rap binding. Plexin stabilizes the switch II region of Rap in an unprecedented conformation, bringing Gln63 in Rap into the active site for catalyzing GTP hydrolysis. The structures also explain the unique Rap-specificity of plexins. Mutational analyses support that these mechanisms underlie plexin activation and signaling. DOI:http://dx.doi.org/10.7554/eLife.01279.001.


    Organizational Affiliation

    Department of Pharmacology , University of Texas Southwestern Medical Center , Dallas , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GCN4 coiled-coil fused zebrafish PlexinC1
A, B
632Danio rerioMutation(s): 0 
Gene Names: plxnc1
Find proteins for Q5RGW1 (Danio rerio)
Go to UniProtKB:  Q5RGW1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.307 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.216α = 90.00
b = 146.100β = 90.00
c = 209.581γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
PHASERphasing
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references