3AJB

Crystal Structure of human Pex3p in complex with N-terminal Pex19p peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p

Sato, Y.Shibata, H.Nakatsu, T.Nakano, H.Kashiwayama, Y.Imanaka, T.Kato, H.

(2010) Embo J. 29: 4083-4093

  • DOI: 10.1038/emboj.2010.293

  • PubMed Abstract: 
  • Peroxisomes require peroxin (Pex) proteins for their biogenesis. The interaction between Pex3p, which resides on the peroxisomal membrane, and Pex19p, which resides in the cytosol, is crucial for peroxisome formation and the post-translational target ...

    Peroxisomes require peroxin (Pex) proteins for their biogenesis. The interaction between Pex3p, which resides on the peroxisomal membrane, and Pex19p, which resides in the cytosol, is crucial for peroxisome formation and the post-translational targeting of peroxisomal membrane proteins (PMPs). It is not known how Pex3p promotes the specific interaction with Pex19p for the purpose of PMP translocation. Here, we present the three-dimensional structure of the complex between a cytosolic domain of Pex3p and the binding-region peptide of Pex19p. The overall shape of Pex3p is a prolate spheroid with a novel fold, the 'twisted six-helix bundle.' The Pex19p-binding site is at an apex of the Pex3p spheroid. A 16-residue region of the Pex19p peptide forms an α-helix and makes a contact with Pex3p; this helix is disordered in the unbound state. The Pex19p peptide contains a characteristic motif, consisting of the leucine triad (Leu18, Leu21, Leu22), and Phe29, which are critical for the Pex3p binding and peroxisome biogenesis.


    Organizational Affiliation

    Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisomal biogenesis factor 3
A
330Homo sapiensMutation(s): 0 
Gene Names: PEX3
Find proteins for P56589 (Homo sapiens)
Go to Gene View: PEX3
Go to UniProtKB:  P56589
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peroxisomal biogenesis factor 19
B
49Homo sapiensMutation(s): 1 
Gene Names: PEX19 (HK33, PXF)
Find proteins for P40855 (Homo sapiens)
Go to Gene View: PEX19
Go to UniProtKB:  P40855
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 147.600α = 90.00
b = 147.600β = 90.00
c = 86.202γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXphasing
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description