1N5Z

Complex structure of Pex13p SH3 domain with a peptide of Pex14p


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Topography for Independent Binding of alpha-Helical and PPII-Helical Ligands to a Peroxisomal SH3 Domain

Douangamath, A.Filipp, F.V.Klein, A.T.J.Barnett, P.Zou, P.Voorn-Brouwer, T.Vega, M.C.Mayans, O.M.Sattler, M.Distel, B.Wilmanns, M.

(2002) Mol Cell 10: 1007-1017

  • DOI: 10.1016/s1097-2765(02)00749-9
  • Primary Citation of Related Structures:  
    1N5Z, 1JQQ

  • PubMed Abstract: 
  • While the function of most small signaling domains is confined to binary ligand interactions, the peroxisomal Pex13p SH3 domain has the unique capacity of binding to two different ligands, Pex5p and Pex14p. We have used this domain as a model to decipher its structurally independent ligand binding sites ...

    While the function of most small signaling domains is confined to binary ligand interactions, the peroxisomal Pex13p SH3 domain has the unique capacity of binding to two different ligands, Pex5p and Pex14p. We have used this domain as a model to decipher its structurally independent ligand binding sites. By the combined use of X-ray crystallography, NMR spectroscopy, and circular dichroism, we show that the two ligands bind in unrelated conformations to patches located at opposite surfaces of this SH3 domain. Mutations in the Pex13p SH3 domain that abolish interactions within the Pex13p-Pex5p interface specifically impair PTS1-dependent protein import into yeast peroxisomes.


    Organizational Affiliation

    EMBL-Hamburg, c/o Deutsches Elektronen Synchrotron, Notkestrasse 85, D-22603 Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisomal membrane protein PAS20AB92Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P80667 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P80667 
Go to UniProtKB:  P80667
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
14-mer peptide from Peroxisomal membrane protein PEX14PQ14N/AMutation(s): 0 
Find proteins for P53112 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53112 
Go to UniProtKB:  P53112
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.35α = 90
b = 63.204β = 90
c = 66.935γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BEASTmodel building
REFMACrefinement
BEASTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance