1HXI | pdb_00001hxi

AN UNEXPECTED EXTENDED CONFORMATION FOR THE THIRD TPR MOTIF OF THE PEROXIN PEX5 FROM TRYPANOSOMA BRUCEI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.223 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1HXI

This is version 1.3 of the entry. See complete history

Literature

An unexpected extended conformation for the third TPR motif of the peroxin PEX5 from Trypanosoma brucei.

Kumar, A.Roach, C.Hirsh, I.S.Turley, S.deWalque, S.Michels, P.A.Hol, W.G.

(2001) J Mol Biology 307: 271-282

  • DOI: https://doi.org/10.1006/jmbi.2000.4465
  • Primary Citation Related Structures: 
    1HXI

  • PubMed Abstract: 

    A number of helix-rich protein motifs are involved in a variety of critical protein-protein interactions in living cells. One of these is the tetratrico peptide repeat (TPR) motif that is involved, amongst others, in cell cycle regulation, chaperone function and post-translation modifications. So far, these helix-rich TPR motifs have always been observed to be a compact unit of two helices interacting with each other in antiparallel fashion. Here, we describe the structure of the first three TPR-motifs of the peroxin PEX5 from Trypanosoma brucei, the causative agent of sleeping sickness. Peroxins are proteins involved in peroxisome, glycosome and glyoxysome biogenesis. PEX5 is the receptor of the proteins targeted to these organelles by the "peroxisomal targeting signal-1", a C-terminal tripeptide called PTS-1. The first two of the three TPR-motifs of T. brucei PEX5 appear to adopt the canonical antiparallel helix hairpin structure. In contrast, the third TPR motif of PEX5 has a dramatically different conformation in our crystals: the two helices that were supposed to form a hairpin are folded into one single 44 A long continuous helix. Such a conformation has never been observed before for a TPR motif. This raises interesting questions including the potential functional importance of a "jack-knife" conformational change in TPR motifs.


  • Organizational Affiliation
    • Departments of Biological Structure and Biochemistry, Biomolecular Structure Center and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 13.74 kDa 
  • Atom Count: 1,022 
  • Modeled Residue Count: 112 
  • Deposited Residue Count: 121 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PEROXISOME TARGETING SIGNAL 1 RECEPTOR PEX5121Trypanosoma bruceiMutation(s): 4 
Gene Names: PEX5
UniProt
Find proteins for Q57W55 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57W55 
Go to UniProtKB:  Q57W55
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57W55
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.223 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75α = 90
b = 75β = 90
c = 56.01γ = 120
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-21
    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: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary