3HM6

Crystal structure of the cytoplasmic domain of human plexin B1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.402 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and function of the intracellular region of the plexin-b1 transmembrane receptor.

Tong, Y.Hota, P.K.Penachioni, J.Y.Hamaneh, M.B.Kim, S.Alviani, R.S.Shen, L.He, H.Tempel, W.Tamagnone, L.Park, H.W.Buck, M.

(2009) J.Biol.Chem. 284: 35962-35972

  • DOI: 10.1074/jbc.M109.056275

  • PubMed Abstract: 
  • Members of the plexin family are unique transmembrane receptors in that they interact directly with Rho family small GTPases; moreover, they contain a GTPase-activating protein (GAP) domain for R-Ras, which is crucial for plexin-mediated regulation o ...

    Members of the plexin family are unique transmembrane receptors in that they interact directly with Rho family small GTPases; moreover, they contain a GTPase-activating protein (GAP) domain for R-Ras, which is crucial for plexin-mediated regulation of cell motility. However, the functional role and structural basis of the interactions between the different intracellular domains of plexins remained unclear. Here we present the 2.4 A crystal structure of the complete intracellular region of human plexin-B1. The structure is monomeric and reveals that the GAP domain is folded into one structure from two segments, separated by the Rho GTPase binding domain (RBD). The RBD is not dimerized, as observed previously. Instead, binding of a conserved loop region appears to compete with dimerization and anchors the RBD to the GAP domain. Cell-based assays on mutant proteins confirm the functional importance of this coupling loop. Molecular modeling based on structural homology to p120(GAP).H-Ras suggests that Ras GTPases can bind to the plexin GAP region. Experimentally, we show that the monomeric intracellular plexin-B1 binds R-Ras but not H-Ras. These findings suggest that the monomeric form of the intracellular region is primed for GAP activity and extend a model for plexin activation.


    Organizational Affiliation

    Departments of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plexin-B1
X
644Homo sapiensMutation(s): 1 
Gene Names: PLXNB1 (KIAA0407, PLXN5, SEP)
Find proteins for O43157 (Homo sapiens)
Go to Gene View: PLXNB1
Go to UniProtKB:  O43157
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Unknown peptide
C
27N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
X
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
C
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.402 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.346α = 90.00
b = 74.346β = 90.00
c = 214.398γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SOLVEphasing
RESOLVEphasing
REFMACrefinement
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description