1JQQ

Crystal structure of Pex13p(301-386) SH3 domain

• PDB DOI: https://doi.org/10.2210/pdb1JQQ/pdb

• Classification: PROTEIN TRANSPORT, MEMBRANE PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-08-08 Released: 2002-12-06 
• Deposition Author(s): Douangamath, A., Mayans, O., Barnett, P., Distel, B., Wilmanns, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.277 
• R-Value Work: 0.235 

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., Sattler, M., Distel, B., Wilmanns, M.

(2002) Mol Cell 10: 1007-1017

• PubMed: 12453410 
• DOI: https://doi.org/10.1016/s1097-2765(02)00749-9
• Primary Citation of Related Structures:  
  1JQQ, 1N5Z


• 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. 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.13 kDa 
• Atom Count: 2,463 
• Modelled Residue Count: 304 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOMAL MEMBRANE PROTEIN PAS20	A, B, C, D	92	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P80667 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P80667  Go to UniProtKB:  P80667

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.277 
• R-Value Work: 0.235 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.199	α = 90
b = 50.441	β = 109.04
c = 74.773	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-06 
Deposition Author(s): Douangamath, A., Mayans, O., Barnett, P., Distel, B., Wilmanns, M.

Revision History  

• Version 1.0: 2002-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references