1W24

Crystal Structure Of human Vps29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Human Vacuolar Protein Sorting Protein 29 Reveals a Phosphodiesterase/Nuclease-Like Fold and Two Protein-Protein Interaction Sites.

Wang, D.Guo, M.Liang, Z.Fan, J.Zhu, Z.Zang, J.Zhu, Z.Li, X.Teng, M.Niu, L.Dong, Y.Liu, P.

(2005) J.Biol.Chem. 280: 22962

  • DOI: 10.1074/jbc.M500464200

  • PubMed Abstract: 
  • Vacuolar protein sorting protein 29 (Vps29p), which is involved in retrograde trafficking from prevacuolar endosomes to the trans-Golgi network, performs its biological functions by participating in the formation of a "retromer complex." In human cel ...

    Vacuolar protein sorting protein 29 (Vps29p), which is involved in retrograde trafficking from prevacuolar endosomes to the trans-Golgi network, performs its biological functions by participating in the formation of a "retromer complex." In human cells, this complex comprises four conserved proteins: hVps35p, hVps29p, hVps26p, and sorting nexin 1 protein (SNX1). Here, we report the crystal structure of hVps29p at 2.1 Angstroms resolution, the first three-dimensional structure of the retromer subunits. This novel structure adopts a four-layered alpha-beta-beta-alpha sandwich fold. hVps29p contains a metal-binding site that is very similar to the active sites of some proteins of the phosphodiesterase/nuclease protein family, indicating that hVps29p may carry out chemically similar functions. Structure and sequence conservation analysis suggests that hVps29p contains two protein-protein interaction sites. One site, which potentially serves as the interface between hVps29p and hVps35p, comprises 5 conserved hydrophobic and 8 hydrophilic residues. The other site is relatively more hydrophilic and may serve as a binding interface with hVps26p, SNX1, or other target proteins.


    Organizational Affiliation

    Hefei National Laboratory of Physical Sciences at Microscale, Key Laboratory of Structural Biology of Chinese Academy of Sciences.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VACUOLAR PROTEIN SORTING PROTEIN 29
A
182Homo sapiensMutation(s): 0 
Gene Names: VPS29
Find proteins for Q9UBQ0 (Homo sapiens)
Go to Gene View: VPS29
Go to UniProtKB:  Q9UBQ0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.871α = 90.00
b = 53.871β = 90.00
c = 124.200γ = 90.00
Software Package:
Software NamePurpose
MARSCALEdata scaling
AUTOMARdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Data collection