4M8N

Crystal Structure of PlexinC1/Rap1B Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.294 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.243 

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
PlexinC1 Intracellular Region
A, B, C, D
599Danio rerioMutation(s): 0 
Gene Names: plxnc1
Find proteins for Q5RGW1 (Danio rerio)
Go to UniProtKB:  Q5RGW1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rap-1b
E, F, G, H
199Homo 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
GDP
Query on GDP

Download SDF File 
Download CCD File 
E, F, G, H
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AF3
Query on AF3

Download SDF File 
Download CCD File 
E, F, G, H
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.294 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.243 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 76.276α = 91.09
b = 84.734β = 95.15
c = 138.752γ = 90.32
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data collection
PHASERphasing
PHENIXrefinement
HKL-3000data scaling

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