3HM6

Crystal structure of the cytoplasmic domain of human plexin B1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    3HM6

  • 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 of cell motility ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plexin-B1A [auth X]644Homo sapiensMutation(s): 1 
Gene Names: PLXNB1KIAA0407PLXN5SEP
UniProt & NIH Common Fund Data Resources
Find proteins for O43157 (Homo sapiens)
Explore O43157 
Go to UniProtKB:  O43157
PHAROS:  O43157
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43157
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown peptideB [auth C]27Homo sapiensMutation(s): 0 
Gene Names: PLXNB1KIAA0407PLXN5SEP
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download Ideal Coordinates CCD File 
C [auth X],
D [auth X],
E [auth X],
F [auth X],
G [auth X],
C [auth X],
D [auth X],
E [auth X],
F [auth X],
G [auth X],
H [auth X],
I [auth X],
J [auth X],
K [auth X],
L [auth X],
M [auth X],
N [auth X],
O [auth X],
P [auth X],
Q [auth X],
R [auth X],
S [auth X],
T [auth X],
U [auth X]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.346α = 90
b = 74.346β = 90
c = 214.398γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-10-13
    Changes: Database references, Source and taxonomy