2FAU

Crystal structure of human vps26


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The retromer subunit Vps26 has an arrestin fold and binds Vps35 through its C-terminal domain.

Shi, H.Rojas, R.Bonifacino, J.S.Hurley, J.H.

(2006) Nat.Struct.Mol.Biol. 13: 540-548

  • DOI: 10.1038/nsmb1103

  • PubMed Abstract: 
  • The mammalian retromer complex consists of SNX1, SNX2, Vps26, Vps29 and Vps35, and retrieves lysosomal enzyme receptors from endosomes to the trans-Golgi network. The structure of human Vps26A at 2.1-A resolution reveals two curved beta-sandwich doma ...

    The mammalian retromer complex consists of SNX1, SNX2, Vps26, Vps29 and Vps35, and retrieves lysosomal enzyme receptors from endosomes to the trans-Golgi network. The structure of human Vps26A at 2.1-A resolution reveals two curved beta-sandwich domains connected by a polar core and a flexible linker. Vps26 has an unpredicted structural relationship to arrestins. The Vps35-binding site on Vps26 maps to a mobile loop spanning residues 235-246, near the tip of the C-terminal domain. The loop is phylogenetically conserved and provides a mechanism for Vps26 integration into the complex that leaves the rest of the structure free for engagements with membranes and for conformational changes. Hydrophobic residues and a glycine in this loop are required for integration into the retromer complex and endosomal localization of human Vps26, and for the function of yeast Vps26 in carboxypeptidase Y sorting.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting 26
A
341Homo sapiensMutation(s): 0 
Gene Names: VPS26A (VPS26)
Find proteins for O75436 (Homo sapiens)
Go to Gene View: VPS26A
Go to UniProtKB:  O75436
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAF
Query on CAF
A
L-PEPTIDE LINKINGC5 H12 As N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.964α = 90.00
b = 76.368β = 90.00
c = 126.491γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SOLVEphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance