5E6P

PlexinB2 cytoplasmic region/PDZ-RhoGEF PDZ domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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 U S A 112: 14852-14857

  • DOI: https://doi.org/10.1073/pnas.1508931112
  • Primary Citation of Related Structures:  
    5E6P

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plexin-B2621Mus musculusMutation(s): 0 
Gene Names: Plxnb2
UniProt & NIH Common Fund Data Resources
Find proteins for B2RXS4 (Mus musculus)
Explore B2RXS4 
Go to UniProtKB:  B2RXS4
IMPC:  MGI:2154239
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RXS4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rho guanine nucleotide exchange factor 1188Homo sapiensMutation(s): 0 
Gene Names: ARHGEF11KIAA0380
UniProt & NIH Common Fund Data Resources
Find proteins for O15085 (Homo sapiens)
Explore O15085 
Go to UniProtKB:  O15085
PHAROS:  O15085
GTEx:  ENSG00000132694 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15085
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.152α = 90
b = 126.152β = 90
c = 211.465γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-3000data collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM088197
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM031954
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM008203

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description