3RYT

The Plexin A1 intracellular region in complex with Rac1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.582 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Plexins Are GTPase-Activating Proteins for Rap and Are Activated by Induced Dimerization.

Wang, Y., He, H., Srivastava, N., Vikarunnessa, S., Chen, Y.B., Jiang, J., Cowan, C.W., Zhang, X.

(2012) Sci.Signal. 5: ra6-ra6

  • DOI: 10.1126/scisignal.2002636

  • PubMed Abstract: 

    • Plexins are cell surface receptors that bind to semaphorins and transduce signals that regulate neuronal development, immune responses, and other processes. Signaling through plexins has been proposed to rely on specific guanosine triphosphatase (GTP ...

    Plexins are cell surface receptors that bind to semaphorins and transduce signals that regulate neuronal development, immune responses, and other processes. Signaling through plexins has been proposed to rely on specific guanosine triphosphatase (GTPase)-activating protein (GAP) activity for R-Ras and M-Ras. Activation of this GAP activity of plexins appears to require simultaneous binding of semaphorin to the plexin extracellular domain and of the Rho GTPases Rac1 or Rnd1 to the cytoplasmic region. However, GAP activity of plexins has eluded detection in several recent studies. We show that the purified cytoplasmic region of plexin uses a noncanonical catalytic mechanism to act as a GAP for Rap, but not for R-Ras or M-Ras. The RapGAP activity of plexins was autoinhibited and was activated by induced dimerization. Biochemical and crystallographic analyses demonstrated that binding of Rho GTPases did not directly contribute to activation of plexin RapGAP activity. Semaphorin stimulated the RapGAP activity of full-length plexin in cells, which was required for plexin-mediated neuronal growth cone collapse. Together, these findings define a pathway for plexin signaling and provide insights into the mechanism for semaphorin-induced activation of plexins.

    Organizational Affiliation: 

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75063, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plexin-A1
A, B
626Mus musculusMutation(s): 0 
Gene Names: Plxna1 (Kiaa4053)
Find proteins for P70206 (Mus musculus)
Go to UniProtKB:  P70206
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ras-related C3 botulinum toxin substrate 1
C
180Homo sapiensMutation(s): 1 
Gene Names: RAC1 (TC25)
Find proteins for P63000 (Homo sapiens)
Go to Gene View: RAC1
Go to UniProtKB:  P63000
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP
Download SDF File 
Download CCD File 
C
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.582 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.270 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.783α = 90.00
b = 110.783β = 90.00
c = 265.628γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-05-11 
  • Released Date: 2012-01-18 
  • Deposition Author(s): Zhang, X., He, H.

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Database references