5I7Z

Crystal structure of a Par-6 PDZ-Crumbs 3 C-terminal peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding of Crumbs to the Par-6 CRIB-PDZ Module Is Regulated by Cdc42.

Whitney, D.S.Peterson, F.C.Kittell, A.W.Egner, J.M.Prehoda, K.E.Volkman, B.F.

(2016) Biochemistry 55: 1455-1461

  • DOI: 10.1021/acs.biochem.5b01342
  • Primary Citation of Related Structures:  
    5I7Z

  • PubMed Abstract: 
  • Par-6 is a scaffold protein that organizes other proteins into a complex required to initiate and maintain cell polarity. Cdc42-GTP binds the CRIB module of Par-6 and alters the binding affinity of the adjoining PDZ domain. Allosteric regulation of the Par-6 PDZ domain was first demonstrated using a peptide identified in a screen of typical carboxyl-terminal ligands ...

    Par-6 is a scaffold protein that organizes other proteins into a complex required to initiate and maintain cell polarity. Cdc42-GTP binds the CRIB module of Par-6 and alters the binding affinity of the adjoining PDZ domain. Allosteric regulation of the Par-6 PDZ domain was first demonstrated using a peptide identified in a screen of typical carboxyl-terminal ligands. Crumbs, a membrane protein that localizes a conserved polarity complex, was subsequently identified as a functional partner for Par-6 that likely interacts with the PDZ domain. Here we show by nuclear magnetic resonance that Par-6 binds a Crumbs carboxyl-terminal peptide and report the crystal structure of the PDZ-peptide complex. The Crumbs peptide binds Par-6 more tightly than the previously studied carboxyl peptide ligand and interacts with the CRIB-PDZ module in a Cdc42-dependent manner. The Crumbs:Par-6 crystal structure reveals specific PDZ-peptide contacts that contribute to its higher affinity and Cdc42-enhanced binding. Comparisons with existing structures suggest that multiple C-terminal Par-6 ligands respond to a common conformational switch that transmits the allosteric effects of GTPase binding.


    Organizational Affiliation

    Department of Biochemistry, Medical College of Wisconsin , Milwaukee, Wisconsin 53226, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LD29223pA96Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for O97111 (Drosophila melanogaster)
Explore O97111 
Go to UniProtKB:  O97111
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Crb-3B8Homo sapiensMutation(s): 0 
Gene Names: CRB3UNQ588/PRO1158
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUF7 (Homo sapiens)
Explore Q9BUF7 
Go to UniProtKB:  Q9BUF7
PHAROS:  Q9BUF7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.06α = 90
b = 65.06β = 90
c = 52.596γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI058072
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM068032

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence