5F0K

Structure of VPS35 N terminal region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Mechanism for Cargo Recognition by the Retromer Complex.

Lucas, M.Gershlick, D.C.Vidaurrazaga, A.Rojas, A.L.Bonifacino, J.S.Hierro, A.

(2016) Cell 167: 1623-1635.e14

  • DOI: https://doi.org/10.1016/j.cell.2016.10.056
  • Primary Citation of Related Structures:  
    5F0J, 5F0K, 5F0L, 5F0M, 5F0P

  • PubMed Abstract: 

    Retromer is a multi-protein complex that recycles transmembrane cargo from endosomes to the trans-Golgi network and the plasma membrane. Defects in retromer impair various cellular processes and underlie some forms of Alzheimer's disease and Parkinson's disease. Although retromer was discovered over 15 years ago, the mechanisms for cargo recognition and recruitment to endosomes have remained elusive. Here, we present an X-ray crystallographic analysis of a four-component complex comprising the VPS26 and VPS35 subunits of retromer, the sorting nexin SNX3, and a recycling signal from the divalent cation transporter DMT1-II. This analysis identifies a binding site for canonical recycling signals at the interface between VPS26 and SNX3. In addition, the structure highlights a network of cooperative interactions among the VPS subunits, SNX3, and cargo that couple signal-recognition to membrane recruitment.


  • Organizational Affiliation

    Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 35
A, B, C, D, E
462Homo sapiensMutation(s): 0 
Gene Names: VPS35MEM3TCCCTA00141
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QK1 (Homo sapiens)
Explore Q96QK1 
Go to UniProtKB:  Q96QK1
PHAROS:  Q96QK1
GTEx:  ENSG00000069329 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QK1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
V [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
FA [auth E],
L [auth A],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
EA [auth E]
K [auth A]
O [auth B]
AA [auth D],
DA [auth E],
EA [auth E],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
U [auth C],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth E]
F [auth A]
G [auth A]
H [auth A]
BA [auth E],
CA [auth E],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
S [auth C],
T [auth C],
W [auth D],
X [auth D],
Y [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.7α = 90
b = 108.6β = 125.5
c = 167.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BUCCANEERmodel building
SHELXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Carlos III Health InstituteSpainBFU2014-59759-R
Basque GovernmentSpainPI2011-26
Spanish Ministry of Economy and CompetitivenessSpainBFU2014-59759-R

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references