5DFZ Transferase date Aug 27, 2015
title Structure Of Vps34 Complex II From S. Cerevisiae.
authors K.Rostislavleva, N.Soler, Y.Ohashi, L.Zhang, R.L.Williams
compound source
Molecule: Vacuolar Protein Sorting-Associated Protein 38
Chain: A
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Vps38, Vpl17, Ylr360w, L8039.11
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932

Molecule: Phosphatidylinositol 3-Kinase Vps34
Chain: C
Synonym: Ptdins-3-Kinase Vps34,Carboxypeptidase Y-Deficient 15,Vacuolar Protein Sorting-Associated Protein 34,Vacuolar Targeting Protein 29;
Ec: 2.7.1.137
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Vps34, End12, Pep15, Vpl7, Vpt29, Ylr240w, L9672.10
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932

Molecule: Serinethreonine-Protein Kinase Vps15
Chain: B
Synonym: Golgi-Retention Defective Mutant Protein 8,Vacuola Sorting-Associated Protein 15;
Ec: 2.7.11.1
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Vps15, Grd8, Vac4, Vpl19, Ybr097w, Ybr0825
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932

Molecule: Nanobody Binding S. Cerevisiae Vps34
Chain: E
Engineered: Yes
Organism_scientific: Lama Glama
Organism_taxid: 9844
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Vacuolar Protein Sorting-Associated Protein 30
Chain: D
Synonym: Autophagy-Related Protein 6
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Vps30, Apg6, Atg6, Vpt30, Ypl120w, Lph7
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932

Molecule: Putative N-Terminal Domain Of S. Cerevisiae Vps30
Chain: G
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932
symmetry Space Group: P 21 21 2
R_factor 0.368 R_Free 0.376
crystal
cell
length a length b length c angle alpha angle beta angle gamma
215.180 226.840 127.210 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.40 Å
ligand
enzyme Transferase E.C.2.7.1.137 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


Primary referenceStructure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes., Rostislavleva K, Soler N, Ohashi Y, Zhang L, Pardon E, Burke JE, Masson GR, Johnson C, Steyaert J, Ktistakis NT, Williams RL, Science. 2015 Oct 9;350(6257):aac7365. doi: 10.1126/science.aac7365. PMID:26450213
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (319 Kb) [Save to disk]
  • Biological Unit Coordinates (5dfz.pdb1.gz) 294 Kb
  • CSU: Contacts of Structural Units for 5DFZ
  • Structure Factors (986 Kb)
  • Retrieve 5DFZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DFZ from S2C, [Save to disk]
  • Re-refined 5dfz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5DFZ 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 5DFZ
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dfz_G] [5dfz_E] [5dfz_D] [5dfz_C] [5dfz_A] [5dfz_B] [5dfz]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5DFZ: [IGv] [PI3K_C2] [PI3Ka] [PI3Kc] [STYKc] [WD40 ] by SMART
    • Other resources with information on 5DFZ
  • Community annotation for 5DFZ at PDBWiki (http://pdbwiki.org)

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