5F0L

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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

  • 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 ...

    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; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain. Electronic address: ahierro@cicbiogune.es.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 35A462Homo sapiensMutation(s): 0 
Gene Names: VPS35MEM3TCCCTA00141
Find proteins for Q96QK1 (Homo sapiens)
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Go to UniProtKB:  Q96QK1
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PHAROS:  Q96QK1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 26AB317Homo sapiensMutation(s): 0 
Gene Names: VPS26AVPS26
Find proteins for O75436 (Homo sapiens)
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PHAROS:  O75436
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sorting nexin-3C167Homo sapiensMutation(s): 0 
Gene Names: SNX3
Find proteins for O60493 (Homo sapiens)
Explore O60493 
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PHAROS:  O60493
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Natural resistance-associated macrophage protein 2D24Homo sapiensMutation(s): 0 
Gene Names: SLC11A2DCT1DMT1NRAMP2OK/SW-cl.20
Find proteins for P49281 (Homo sapiens)
Explore P49281 
Go to UniProtKB:  P49281
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PHAROS:  P49281
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , FA [auth C] , G [auth A] , GA [auth C] , HA [auth C] , P [auth B] , Q [auth B] , 
E [auth A],  F [auth A],  FA [auth C],  G [auth A],  GA [auth C],  HA [auth C],  P [auth B],  Q [auth B],  R [auth B],  S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], IA [auth C], JA [auth C], T [auth B], U [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , DA [auth B] , EA [auth B] , J [auth A] , K [auth A] , KA [auth C] , 
AA [auth B],  BA [auth B],  CA [auth B],  DA [auth B],  EA [auth B],  J [auth A],  K [auth A],  KA [auth C],  L [auth A],  LA [auth C],  M [auth A],  N [auth A],  O [auth A],  V [auth B],  W [auth B],  X [auth B],  Y [auth B],  Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 371.37α = 90
b = 75.21β = 98.56
c = 57.45γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Carlos III Health InstituteSpainPI11/00121
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