5F0K | pdb_00005f0k

Structure of VPS35 N terminal region

PDB DOI: https://doi.org/10.2210/pdb5F0K/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.07 Å
R-Value Free:
0.255 (Depositor), 0.256 (DCC)
R-Value Work:
0.206 (Depositor), 0.205 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 27889239 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2016.10.056
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 268.62 kDa
Atom Count: 17,611
Modeled Residue Count: 2,158
Deposited Residue Count: 2,310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 35	A, B, C, D, E	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 GTEx: ENSG00000069329
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96QK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain L [auth A] SDF format, chain FA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain FA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain FA [auth E]	FA [auth E], L [auth A], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth E] Focus chain L [auth A] Focus chain R [auth B] Interactions & Density Focus chain FA [auth E] Focus chain L [auth A] Focus chain R [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain AA [auth D]	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		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain CA [auth E] SDF format, chain BA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E]	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		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]