5F0P Protein Transport date Nov 27, 2015
title Structure Of Retromer Vps26-Vps35 Subunits Bound To Snx3 And Dmt1(L557m) (Semet Labeled)
authors M.Lucas, D.Gershlick, A.Vidaurrazaga, A.L.Rojas, J.S.Bonifacino,
compound source
Molecule: Vacuolar Protein Sorting-Associated Protein 35
Chain: A
Fragment: Residues 14-470
Synonym: Hvps35,Maternal-Embryonic 3,Vesicle Protein Sortin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vps35, Mem3, Tcccta00141
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgst-Parallel2

Molecule: Vacuolar Protein Sorting-Associated Protein 26a
Chain: B
Fragment: Residues 1-321
Synonym: Vesicle Protein Sorting 26a,Hvps26
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vps26a, Vps26
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Sumo3

Molecule: Sorting Nexin-3
Chain: C
Fragment: Residues 1-162
Synonym: Protein Sdp3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snx3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phis-Mbp-Parallel2

Molecule: Natural Resistance-Associated Macrophage Protein
Chain: D
Synonym: Nramp 2,Divalent Cation Transporter 1,Divalent Met Transporter 1,Dmt-1,Solute Carrier Family 11 Member 2, Diva Cation Transporter II;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Slc11a2, Dct1, Dmt1, Nramp2, Oksw-Cl.20
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Sumo3
symmetry Space Group: C 1 2 1
R_factor 0.219 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
371.290 75.320 57.270 90.00 97.66 90.00
method X-Ray Diffractionresolution 2.78 Å
ligand EDO, GOL, MSE, SO4, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


Primary referenceStructural Mechanism for Cargo Recognition by the Retromer Complex., Lucas M, Gershlick DC, Vidaurrazaga A, Rojas AL, Bonifacino JS, Hierro A, Cell. 2016 Dec 1;167(6):1623-1635.e14. doi: 10.1016/j.cell.2016.10.056. Epub 2016, Nov 23. PMID:27889239
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (163 Kb) [Save to disk]
  • Biological Unit Coordinates (5f0p.pdb1.gz) 156 Kb
  • LPC: Ligand-Protein Contacts for 5F0P
  • CSU: Contacts of Structural Units for 5F0P
  • Structure Factors (1135 Kb)
  • Retrieve 5F0P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5F0P from S2C, [Save to disk]
  • Re-refined 5f0p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5F0P in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5F0P
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5f0p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5f0p_D] [5f0p_C] [5f0p_B] [5f0p] [5f0p_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5F0P
  • Community annotation for 5F0P at PDBWiki (http://pdbwiki.org)

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