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- PDB-9orm: The structure of human Vacuolar Protein Sorting 34 catalytic doma... -

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Basic information

Entry
Database: PDB / ID: 9orm
TitleThe structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-137
ComponentsPhosphatidylinositol 3-kinase catalytic subunit type 3
KeywordsTRANSFERASE / Phosophatidylinositol-3-Phosphate / lipid regulator / autophagy / membrane trafficking / endocytosis / enzyme
Function / homology
Function and homology information


positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / 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 / presynaptic endosome / host-mediated activation of viral genome replication ...positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / 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 / presynaptic endosome / host-mediated activation of viral genome replication / phosphatidylinositol kinase activity / Synthesis of PIPs at the Golgi membrane / early endosome to late endosome transport / protein localization to phagophore assembly site / response to L-leucine / protein targeting to lysosome / endosome organization / pexophagy / positive regulation of natural killer cell mediated cytotoxicity / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / autolysosome / PI3K Cascade / RHO GTPases Activate NADPH Oxidases / regulation of macroautophagy / autophagosome maturation / axoneme / synaptic vesicle endocytosis / autophagosome assembly / cellular response to glucose starvation / autophagosome / regulation of cytokinesis / regulation of autophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein processing / GABA-ergic synapse / autophagy / phagocytic vesicle membrane / endocytosis / late endosome / peroxisome / midbody / Translation of Replicase and Assembly of the Replication Transcription Complex / protein kinase activity / endosome / cell division / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase, Vps34 type / : / 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 3-kinase, Vps34 type / : / 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-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsBurtch, M. / Abiodun, W. / Litchfield, C. / Cartwright, J. / Doukov, T. / Moody, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM155011 United States
CitationJournal: To Be Published
Title: The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-137
Authors: Burtch, M. / Abiodun, W. / Litchfield, C. / Cartwright, J. / Dass, R. / Singleton, J.D. / Doukov, T. / Peterson, M.A. / Moody, J.D.
History
DepositionMay 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,08312
Polymers68,1501
Non-polymers93411
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.402, 113.402, 145.946
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphatidylinositol 3-kinase catalytic subunit type 3 / PI3-kinase type 3 / PI3K type 3 / PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 ...PI3-kinase type 3 / PI3K type 3 / PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase class 3 / hVps34


Mass: 68149.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3, VPS34 / Plasmid: pET42_SUMO / Details (production host): Kanamycin Resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase

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Non-polymers , 5 types, 191 molecules

#2: Chemical ChemComp-A1CD6 / ethyl 2-[(8S)-pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-benzothiazole-6-carboxylate


Mass: 324.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.32 % / Description: Hexagonal Prism
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 12, 2024
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.06→61.37 Å / Num. obs: 59359 / % possible obs: 99.85 % / Redundancy: 27.3 % / Biso Wilson estimate: 48.48 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.09628 / Rpim(I) all: 0.01872 / Net I/σ(I): 22.56
Reflection shellResolution: 2.06→2.134 Å / Rmerge(I) obs: 3.689 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 5811 / CC1/2: 0.441 / CC star: 0.783 / Rpim(I) all: 0.7036 / Rrim(I) all: 3.756

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→61.37 Å / SU ML: 0.2304 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2271 3045 5.13 %
Rwork0.2065 56270 -
obs0.2076 59315 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.11 Å2
Refinement stepCycle: LAST / Resolution: 2.06→61.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 50 180 4486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834454
X-RAY DIFFRACTIONf_angle_d0.93416026
X-RAY DIFFRACTIONf_chiral_restr0.054670
X-RAY DIFFRACTIONf_plane_restr0.0085776
X-RAY DIFFRACTIONf_dihedral_angle_d14.82241691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.090.30241300.29622480X-RAY DIFFRACTION99.35
2.09-2.130.3441360.29482520X-RAY DIFFRACTION99.55
2.13-2.160.33371450.28842507X-RAY DIFFRACTION99.74
2.16-2.20.28021360.27222503X-RAY DIFFRACTION99.7
2.2-2.240.29491170.2582540X-RAY DIFFRACTION99.81
2.24-2.290.26971460.24892504X-RAY DIFFRACTION99.85
2.29-2.340.29011550.23932504X-RAY DIFFRACTION99.81
2.34-2.390.28361400.23442541X-RAY DIFFRACTION100
2.39-2.450.27111200.2422538X-RAY DIFFRACTION99.85
2.45-2.520.24761300.23392557X-RAY DIFFRACTION99.85
2.52-2.590.28471490.23772514X-RAY DIFFRACTION99.92
2.59-2.680.27621270.23692561X-RAY DIFFRACTION99.93
2.68-2.770.26291380.23492538X-RAY DIFFRACTION99.93
2.77-2.890.29391260.25882562X-RAY DIFFRACTION99.96
2.89-3.020.24691480.24022539X-RAY DIFFRACTION99.96
3.02-3.180.26361190.24372587X-RAY DIFFRACTION99.96
3.18-3.370.27371370.22692571X-RAY DIFFRACTION100
3.37-3.640.2241470.21462574X-RAY DIFFRACTION100
3.64-40.19151460.1862583X-RAY DIFFRACTION100
4-4.580.17091470.16312614X-RAY DIFFRACTION100
4.58-5.770.20531640.17162637X-RAY DIFFRACTION100
5.77-61.370.19891420.18342796X-RAY DIFFRACTION99.73

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