3SUA

Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.39 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


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

Literature

A Dual Binding Mode for RhoGTPases in Plexin Signalling.

Bell, C.H., Aricescu, A.R., Jones, E.Y., Siebold, C.

(2011) Plos Biol. 9: e1001134-e1001134

  • DOI: 10.1371/journal.pbio.1001134
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Plexins are cell surface receptors for the semaphorin family of cell guidance cues. The cytoplasmic region comprises a Ras GTPase-activating protein (GAP) domain and a RhoGTPase binding domain. Concomitant binding of extracellular semaphorin and intr ...

    Plexins are cell surface receptors for the semaphorin family of cell guidance cues. The cytoplasmic region comprises a Ras GTPase-activating protein (GAP) domain and a RhoGTPase binding domain. Concomitant binding of extracellular semaphorin and intracellular RhoGTPase triggers GAP activity and signal transduction. The mechanism of this intricate regulation remains elusive. We present two crystal structures of the human Plexin-B1 cytoplasmic region in complex with a constitutively active RhoGTPase, Rac1. The structure of truncated Plexin-B1-Rac1 complex provides no mechanism for coupling RhoGTPase and Ras binding sites. On inclusion of the juxtamembrane helix, a trimeric structure of Plexin-B1-Rac1 complexes is stabilised by a second, novel, RhoGTPase binding site adjacent to the Ras site. Site-directed mutagenesis combined with cellular and biophysical assays demonstrate that this new binding site is essential for signalling. Our findings are consistent with a model in which extracellular and intracellular plexin clustering events combine into a single signalling output.

    Organizational Affiliation: 

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related C3 botulinum toxin substrate 1
A, B, C
184Homo sapiensMutation(s): 0 
Gene Names: RAC1 (TC25)
Find proteins for P63000 (Homo sapiens)
Go to Gene View: RAC1
Go to UniProtKB:  P63000
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Plexin-B1
D, E, F
633Homo sapiensMutation(s): 0 
Gene Names: PLXNB1 (KIAA0407, PLXN5, SEP)
Find proteins for O43157 (Homo sapiens)
Go to Gene View: PLXNB1
Go to UniProtKB:  O43157
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP
Download SDF File 
Download CCD File 
A, B, 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: 4.39 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.234 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 142.340α = 90.00
b = 224.250β = 90.00
c = 258.160γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2011-10-05
    Type: Database references