Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.93 kDa 
• Atom Count: 7630 
• Modelled Residue Count: 913 
• Deposited Residue Count: 968 
• Unique protein chains: 4

5F0P

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled)

• PDB DOI: 10.2210/pdb5F0P/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-11-27 Released: 2016-12-07 
• Deposition Author(s): Lucas, M., Gershlick, D., Vidaurrazaga, A., Rojas, A.L., Bonifacino, J.S., Hierro, A.
• Funding Organization(s): Carlos III Health Institute, Basque Government, Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.261 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

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

• PubMed: 27889239 
• DOI: 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.

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Organizational Affiliation: 

Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 35	A	462	Homo sapiens	Mutation(s): 0  Gene Names: VPS35, MEM3, TCCCTA00141
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QK1 (Homo sapiens) Explore Q96QK1  Go to UniProtKB:  Q96QK1
PHAROS:  Q96QK1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 26A	B	321	Homo sapiens	Mutation(s): 0  Gene Names: VPS26A, VPS26
UniProt & NIH Common Fund Data Resources
Find proteins for O75436 (Homo sapiens) Explore O75436  Go to UniProtKB:  O75436
PHAROS:  O75436

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting nexin-3	C	167	Homo sapiens	Mutation(s): 0  Gene Names: SNX3
UniProt & NIH Common Fund Data Resources
Find proteins for O60493 (Homo sapiens) Explore O60493  Go to UniProtKB:  O60493
PHAROS:  O60493

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Natural resistance-associated macrophage protein 2	D	18	Homo sapiens	Mutation(s): 1  Gene Names: SLC11A2, DCT1, DMT1, NRAMP2, OK/SW-cl.20
UniProt & NIH Common Fund Data Resources
Find proteins for P49281 (Homo sapiens) Explore P49281  Go to UniProtKB:  P49281
PHAROS:  P49281

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], FA [auth C], GA [auth C], HA [auth C], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	DA [auth B], G [auth A], H [auth A], R [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	EA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth B], BA [auth B], CA [auth B], I [auth A], IA [auth C], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.261 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 371.29	α = 90
b = 75.32	β = 97.66
c = 57.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-27 
• Released Date: 2016-12-07 
Deposition Author(s): Lucas, M., Gershlick, D., Vidaurrazaga, A., Rojas, A.L., Bonifacino, J.S., Hierro, A.

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Funding Organization	Location	Grant Number
Carlos III Health Institute	Spain	PI11/00121
Basque Government	Spain	PI2011-26
Spanish Ministry of Economy and Competitiveness	Spain	BFU2014-59759-R

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Database references
• Version 1.2: 2017-11-29
  Changes: Database references