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- PDB-4oys: CRYSTAL STRUCTURE OF VPS34 IN COMPLEX WITH SAR405. -

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Basic information

Entry
Database: PDB / ID: 4oys
TitleCRYSTAL STRUCTURE OF VPS34 IN COMPLEX WITH SAR405.
ComponentsPhosphatidylinositol 3-kinase catalytic subunit type 3
KeywordsLIPID KINASE
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity ...Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / protein targeting to lysosome / early endosome to late endosome transport / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / Macroautophagy / 1-phosphatidylinositol-3-kinase activity / axoneme / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / autophagosome maturation / autophagosome assembly / PI3K Cascade / RHO GTPases Activate NADPH Oxidases / autophagosome / regulation of macroautophagy / cellular response to glucose starvation / regulation of cytokinesis / regulation of autophagy / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / autophagy / endocytosis / phagocytic vesicle membrane / peroxisome / late endosome / kinase activity / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / protein kinase activity / endosome / cell cycle / phosphorylation / cell division / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase, Vps34 type / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. ...Phosphatidylinositol 3-kinase, Vps34 type / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-1TT / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMathieu, M. / Marquette, J.p.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy.
Authors: Ronan, B. / Flamand, O. / Vescovi, L. / Dureuil, C. / Durand, L. / Fassy, F. / Bachelot, M.F. / Lamberton, A. / Mathieu, M. / Bertrand, T. / Marquette, J.P. / El-Ahmad, Y. / Filoche-Romme, B. ...Authors: Ronan, B. / Flamand, O. / Vescovi, L. / Dureuil, C. / Durand, L. / Fassy, F. / Bachelot, M.F. / Lamberton, A. / Mathieu, M. / Bertrand, T. / Marquette, J.P. / El-Ahmad, Y. / Filoche-Romme, B. / Schio, L. / Garcia-Echeverria, C. / Goulaouic, H. / Pasquier, B.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jun 6, 2018Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Mar 27, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3-kinase catalytic subunit type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4286
Polymers68,5971
Non-polymers8305
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-53 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.810, 145.700, 61.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phosphatidylinositol 3-kinase catalytic subunit type 3 / PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase ...PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase class 3 / hVps34


Mass: 68597.391 Da / Num. of mol.: 1 / Fragment: UNP residues 282-879
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3,VPS34 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1TT / (8S)-9-[(5-chloranylpyridin-3-yl)methyl]-2-[(3R)-3-methylmorpholin-4-yl]-8-(trifluoromethyl)-6,7,8,9a-tetrahydro-3H-pyrimido[1,2-a]pyrimidin-4-one


Mass: 445.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23ClF3N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.9 M ammonium sulfate, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.9→89.91 Å / Num. obs: 18671 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 66.27 Å2 / Rsym value: 0.209 / Net I/σ(I): 8.8
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameClassification
PROCESSdata reduction
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house

Resolution: 2.9→72.85 Å / SU R Cruickshank DPI: 1.58 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 1.784 / SU Rfree Blow DPI: 0.349 / SU Rfree Cruickshank DPI: 0.354
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1002 5.38 %Random selection
Rwork0.18 ---
obs-18629 99.95 %-
Displacement parametersBiso mean: 57.39 Å2
Baniso -1Baniso -2Baniso -3
1--27.1374 Å20 Å20 Å2
2--6.588 Å2-
3---20.5495 Å2
Refine analyzeLuzzati coordinate error obs: 0.352 Å
Refinement stepCycle: LAST / Resolution: 2.9→72.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 50 16 4535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBOND LENGHTS0.01
X-RAY DIFFRACTIONBOND ANGLES1.13
X-RAY DIFFRACTIONPEPTIDE OMEGA TORSION ANGLES2.57

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