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 
  • R-Value Observed: 0.235 

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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:  
    3SU8, 3SUA

  • 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 intracellular RhoGTPase triggers GAP activity and signal transduction ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related C3 botulinum toxin substrate 1A, B, C184Homo sapiensMutation(s): 0 
Gene Names: RAC1, TC25, MIG5
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens)
Explore P63000 
Go to UniProtKB:  P63000
PHAROS:  P63000
GTEx:  ENSG00000136238 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63000
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Plexin-B1D, E, F633Homo sapiensMutation(s): 0 
Gene Names: PLXNB1, KIAA0407, PLXN5, SEP
UniProt & NIH Common Fund Data Resources
Find proteins for O43157 (Homo sapiens)
Explore O43157 
Go to UniProtKB:  O43157
PHAROS:  O43157
GTEx:  ENSG00000164050 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43157
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
L [auth C]		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-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 
  • R-Value Observed: 0.235 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.34α = 90
b = 224.25β = 90
c = 258.16γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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