1NF3

Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

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This is version 1.4 of the entry. See complete history


Literature

Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6

Garrard, S.M.Capaldo, C.T.Gao, L.Rosen, M.K.Macara, I.G.Tomchick, D.R.

(2003) EMBO J 22: 1125-1133

  • DOI: https://doi.org/10.1093/emboj/cdg110
  • Primary Citation of Related Structures:  
    1NF3

  • PubMed Abstract: 

    Cdc42 is a small GTPase that is required for cell polarity establishment in eukaryotes as diverse as budding yeast and mammals. Par6 is also implicated in metazoan cell polarity establishment and asymmetric cell divisions. Cdc42.GTP interacts with proteins that contain a conserved sequence called a CRIB motif. Uniquely, Par6 possesses a semi-CRIB motif that is not sufficient for binding to Cdc42. An adjacent PDZ domain is also necessary and is required for biological effects of Par6. Here we report the crystal structure of a complex between Cdc42 and the Par6 GTPase-binding domain. The semi-CRIB motif forms a beta-strand that inserts between the four strands of Cdc42 and the three strands of the PDZ domain to form a continuous eight-stranded sheet. Cdc42 induces a conformational change in Par6, detectable by fluorescence resonance energy transfer spectroscopy. Nuclear magnetic resonance studies indicate that the semi-CRIB motif of Par6 is at least partially structured by the PDZ domain. The structure highlights a novel role for a PDZ domain as a structural scaffold.


  • Organizational Affiliation

    Center for Cell Signaling and Department of Microbiology, University of Virginia, Charlottesville, VA 22908, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G25K GTP-binding protein, placental isoform
A, B
195Homo sapiensMutation(s): 1 
Gene Names: CDC42
UniProt & NIH Common Fund Data Resources
Find proteins for P60953 (Homo sapiens)
Explore P60953 
Go to UniProtKB:  P60953
GTEx:  ENSG00000070831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60953
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PAR-6B
C, D
128Mus musculusMutation(s): 0 
Gene Names: Par6B
UniProt
Find proteins for Q9JK83 (Mus musculus)
Explore Q9JK83 
Go to UniProtKB:  Q9JK83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JK83
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
GNP Binding MOAD:  1NF3 Kd: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.744α = 81.55
b = 53.787β = 76.59
c = 79.521γ = 90.04
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description