5E6P

PlexinB2 cytoplasmic region/PDZ-RhoGEF PDZ domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.215 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ-RhoGEF.

Pascoe, H.G.Gutowski, S.Chen, H.Brautigam, C.A.Chen, Z.Sternweis, P.C.Zhang, X.

(2015) Proc.Natl.Acad.Sci.USA 112: 14852-14857

  • DOI: 10.1073/pnas.1508931112

  • PubMed Abstract: 
  • PDZ domains are abundant protein interaction modules and typically recognize a short motif at the C terminus of their ligands, with a few residues in the motif endowing the binding specificity. The sequence-based rules, however, cannot fully account ...

    PDZ domains are abundant protein interaction modules and typically recognize a short motif at the C terminus of their ligands, with a few residues in the motif endowing the binding specificity. The sequence-based rules, however, cannot fully account for the specificity between the vast number of PDZ domains and ligands in the cell. Plexins are transmembrane receptors that regulate processes such as axon guidance and angiogenesis. Two related guanine nucleotide exchange factors (GEFs), PDZ-RhoGEF and leukemia-associated RhoGEF (LARG), use their PDZ domains to bind class B plexins and play critical roles in signaling. Here, we present the crystal structure of the full-length cytoplasmic region of PlexinB2 in complex with the PDZ domain of PDZ-RhoGEF. The structure reveals that, in addition to the canonical C-terminal motif/PDZ interaction, the 3D domain of PlexinB2 forms a secondary interface with the PDZ domain. Our biophysical and cell-based assays show that the secondary interface contributes to the specific interaction between plexin and PDZ-RhoGEF and to signaling by plexin in the cell. Formation of secondary interfaces may be a general mechanism for increasing affinity and specificity of modular domain-mediated interactions.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plexin-B2
A
621Mus musculusMutation(s): 0 
Gene Names: Plxnb2
Find proteins for B2RXS4 (Mus musculus)
Go to UniProtKB:  B2RXS4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rho guanine nucleotide exchange factor 11
B
88Homo sapiensMutation(s): 0 
Gene Names: ARHGEF11 (KIAA0380)
Find proteins for O15085 (Homo sapiens)
Go to Gene View: ARHGEF11
Go to UniProtKB:  O15085
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.215 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 126.152α = 90.00
b = 126.152β = 90.00
c = 211.465γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM088197
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM031954
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM008203

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations