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- PDB-5dfz: Structure of Vps34 complex II from S. cerevisiae. -

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Basic information

Entry
Database: PDB / ID: 5dfz
TitleStructure of Vps34 complex II from S. cerevisiae.
Components
  • (Vacuolar protein sorting-associated protein ...) x 2
  • Nanobody binding S. cerevisiae Vps34
  • Phosphatidylinositol 3-kinase VPS34
  • Putative N-terminal domain of S. cerevisiae Vps30
  • Serine/threonine-protein kinase VPS15
KeywordsTRANSFERASE / Vps34 / Vps15 / Vps30 / Vps38 / Autophagy / vacuolar protein sorting / Yeast / Complex II / PI3P / kinase / lipid / WD40 / BARA / C2 / coiled-coil / HEAT / nanobody
Function / homology
Function and homology information


Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / lytic vacuole / RHO GTPases Activate NADPH Oxidases / nucleus-vacuole junction / vacuole-isolation membrane contact site / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / vacuole inheritance ...Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / lytic vacuole / RHO GTPases Activate NADPH Oxidases / nucleus-vacuole junction / vacuole-isolation membrane contact site / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / vacuole inheritance / cellular response to potassium ion starvation / Macroautophagy / protein retention in Golgi apparatus / cytoplasm to vacuole targeting by the Cvt pathway / phagophore assembly site membrane / protein targeting to vacuole / late endosome to vacuole transport / pexophagy / phosphatidylinositol biosynthetic process / piecemeal microautophagy of the nucleus / fungal-type vacuole membrane / phagophore assembly site / retrograde transport, endosome to Golgi / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / phosphatidylinositol 3-kinase / SNARE complex assembly / 1-phosphatidylinositol-3-kinase activity / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / autophagosome assembly / phosphatidylinositol 3-kinase binding / mitophagy / SNARE binding / ubiquitin binding / positive regulation of transcription elongation by RNA polymerase II / macroautophagy / autophagy / endocytosis / late endosome / peroxisome / protein transport / protein-macromolecule adaptor activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / endosome / endosome membrane / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting 38 / Vacuolar protein sorting 38 / Vps8 beta-propeller / Serine/threonine-protein kinase Vps15-like / : / VPS15-like, helical domain / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain ...Vacuolar protein sorting 38 / Vacuolar protein sorting 38 / Vps8 beta-propeller / Serine/threonine-protein kinase Vps15-like / : / VPS15-like, helical domain / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Phosphatidylinositol 3-kinase, Vps34 type / HEAT repeat profile. / HEAT, type 2 / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats profile. / WD40 repeats / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeat / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase VPS15 / Phosphatidylinositol 3-kinase VPS34 / Vacuolar protein sorting-associated protein 30 / Vacuolar protein sorting-associated protein 38
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.4 Å
AuthorsRostislavleva, K. / Soler, N. / Ohashi, Y. / Zhang, L. / Williams, R.L.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cambridge Cancer Center PhD fellowship United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K019155/1 United Kingdom
Medical Research Council (United Kingdom)U105184308 United Kingdom
CitationJournal: Science / Year: 2015
Title: Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes.
Authors: Rostislavleva, K. / Soler, N. / Ohashi, Y. / Zhang, L. / Pardon, E. / Burke, J.E. / Masson, G.R. / Johnson, C. / Steyaert, J. / Ktistakis, N.T. / Williams, R.L.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Aug 30, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 38
C: Phosphatidylinositol 3-kinase VPS34
B: Serine/threonine-protein kinase VPS15
E: Nanobody binding S. cerevisiae Vps34
D: Vacuolar protein sorting-associated protein 30
G: Putative N-terminal domain of S. cerevisiae Vps30


Theoretical massNumber of molelcules
Total (without water)400,4906
Polymers400,4906
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)215.180, 226.840, 127.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules AD

#1: Protein Vacuolar protein sorting-associated protein 38


Mass: 51072.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VPS38, VPL17, YLR360W, L8039.11 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05919
#5: Protein Vacuolar protein sorting-associated protein 30 / Autophagy-related protein 6


Mass: 63400.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VPS30, APG6, ATG6, VPT30, YPL120W, LPH7 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02948

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Protein , 2 types, 2 molecules CB

#2: Protein Phosphatidylinositol 3-kinase VPS34 / PtdIns-3-kinase VPS34 / Carboxypeptidase Y-deficient protein 15 / Vacuolar protein sorting- ...PtdIns-3-kinase VPS34 / Carboxypeptidase Y-deficient protein 15 / Vacuolar protein sorting-associated protein 34 / Vacuolar protein-targeting protein 29


Mass: 100973.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VPS34, END12, PEP15, VPL7, VPT29, YLR240W, L9672.10 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22543, phosphatidylinositol 3-kinase
#3: Protein Serine/threonine-protein kinase VPS15 / Golgi-retention defective mutant protein 8 / Vacuolar protein sorting-associated protein 15


Mass: 167082.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VPS15, GRD8, VAC4, VPL19, YBR097W, YBR0825 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P22219, non-specific serine/threonine protein kinase

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Antibody / Protein/peptide , 2 types, 2 molecules EG

#4: Antibody Nanobody binding S. cerevisiae Vps34


Mass: 13772.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#6: Protein/peptide Putative N-terminal domain of S. cerevisiae Vps30


Mass: 4188.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 300 mM sodium acetate pH 5.1, 3% 1,5- Diaminopentanedihydrochloride. grown at 290 K for 5 days
PH range: 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.939270, 1.254380, 1.254860
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.939271
21.254381
31.254861
ReflectionResolution: 4.4→49.9 Å / Num. all: 40224 / Num. obs: 40224 / % possible obs: 99.8 % / Redundancy: 32.2 % / Rsym value: 0.31 / Net I/σ(I): 21
Reflection shellResolution: 4.4→4.58 Å / Redundancy: 15.8 % / Rmerge(I) obs: 4.82 / Mean I/σ(I) obs: 1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
SHARPphasing
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 4.4→50.358 Å / SU ML: 1.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 51.95 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3762 1955 4.86 %
Rwork0.3683 --
obs0.3687 40211 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.4→50.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14160 0 0 0 14160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214137
X-RAY DIFFRACTIONf_angle_d0.70319692
X-RAY DIFFRACTIONf_dihedral_angle_d3.762830
X-RAY DIFFRACTIONf_chiral_restr0.0292748
X-RAY DIFFRACTIONf_plane_restr0.0022830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4-4.510.481150.46432677X-RAY DIFFRACTION100
4.51-4.63190.51671600.47742696X-RAY DIFFRACTION100
4.6319-4.76810.46411510.46492667X-RAY DIFFRACTION100
4.7681-4.92180.45971370.45652701X-RAY DIFFRACTION100
4.9218-5.09760.50151300.44892721X-RAY DIFFRACTION100
5.0976-5.30150.44711480.46122706X-RAY DIFFRACTION100
5.3015-5.54250.47481610.46622689X-RAY DIFFRACTION100
5.5425-5.83430.52571500.46422689X-RAY DIFFRACTION100
5.8343-6.19920.52691340.43672710X-RAY DIFFRACTION100
6.1992-6.67680.40431290.41712754X-RAY DIFFRACTION100
6.6768-7.34690.45611300.40042747X-RAY DIFFRACTION100
7.3469-8.40580.33691390.36292776X-RAY DIFFRACTION100
8.4058-10.57420.27541500.28922776X-RAY DIFFRACTION100
10.5742-50.36110.33951210.33192947X-RAY DIFFRACTION100

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