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- PDB-9dkp: The structure of human vacuolar protein sorting 34 catalytic doma... -

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Basic information

Entry
Database: PDB / ID: 9dkp
TitleThe structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53
ComponentsPhosphatidylinositol 3-kinase catalytic subunit type 3
KeywordsTRANSFERASE / Phosphatidylinositol 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 / host-mediated activation of viral genome replication / presynaptic endosome ...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 / host-mediated activation of viral genome replication / presynaptic endosome / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / early endosome to late endosome transport / response to L-leucine / protein localization to phagophore assembly site / protein targeting to lysosome / endosome organization / pexophagy / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / phosphatidylinositol-3-phosphate biosynthetic process / phosphatidylinositol 3-kinase / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / autolysosome / PI3K Cascade / axoneme / autophagosome assembly / autophagosome maturation / RHO GTPases Activate NADPH Oxidases / synaptic vesicle endocytosis / regulation of macroautophagy / cellular response to glucose starvation / autophagosome / regulation of cytokinesis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / protein processing / autophagy / phagocytic vesicle membrane / endocytosis / peroxisome / late endosome / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / protein kinase activity / endosome / regulation of autophagy / cell division / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / ATP binding / 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 kinase ...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
: / 2-ETHOXYETHANOL / diethyl ether / : / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsAbiodun, W.O. / Tsubaki, E. / Dass, R. / Singleton, J.D. / Samarawickrama, P. / Doukov, T. / Peterson, M.A. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209 United States
CitationJournal: To Be Published
Title: Facile Bacterial Production of Human Vacuolar Protein Sorting 34 Enables Structural Characterization of Novel Inhibitors
Authors: Abiodun, W.O. / Dass, R. / Tsubaki, E. / Singleton, J.D. / Fullmer, A. / Cartwright, J. / Litchfield, C. / Samarawickrama, P. / Doukov, T. / Peterson, M.A. / Moody, J.D.
History
DepositionSep 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,25821
Polymers68,1501
Non-polymers1,10820
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.506, 113.506, 145.235
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
Components on special symmetry positions
IDModelComponents
11B-904-

ETZ

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Components

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Protein , 1 types, 1 molecules B

#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 , 7 types, 132 molecules

#2: Chemical ChemComp-A1A6F / (8R)-3-(1,3-benzothiazol-2-yl)pyrazolo[1,5-a]pyrimidine


Mass: 252.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H8N4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-ETZ / diethyl ether


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.44 Å3/Da / Density % sol: 64.2 % / Description: Hexagonal Prisms
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 20% PEG, 0.2M MES pH 6.0

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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: Dec 19, 2023
Details: Rh coated collimating mirrors, K-B focusing mirrors
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: 2.16→53.85 Å / Num. obs: 51494 / % possible obs: 99.98 % / Redundancy: 27.5 % / Biso Wilson estimate: 56.6 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1164 / Rpim(I) all: 0.02246 / Rrim(I) all: 0.1185 / Net I/σ(I): 13.99
Reflection shellResolution: 2.16→2.237 Å / Redundancy: 28.5 % / Rmerge(I) obs: 3.425 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 5068 / CC1/2: 0.48 / CC star: 0.805 / Rpim(I) all: 0.6498 / Rrim(I) all: 3.486 / % possible all: 99.98

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Processing

Software
NameVersionClassification
Coot1.20.1_4487model building
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→53.85 Å / SU ML: 0.3413 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 2502 4.86 %
Rwork0.2068 48986 -
obs0.2082 51488 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.47 Å2
Refinement stepCycle: LAST / Resolution: 2.16→53.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 53 112 4279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374314
X-RAY DIFFRACTIONf_angle_d0.60565863
X-RAY DIFFRACTIONf_chiral_restr0.0393662
X-RAY DIFFRACTIONf_plane_restr0.0047765
X-RAY DIFFRACTIONf_dihedral_angle_d13.92941592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.20.39871250.35552703X-RAY DIFFRACTION99.96
2.2-2.250.34041500.32442657X-RAY DIFFRACTION100
2.25-2.30.35411230.30422690X-RAY DIFFRACTION100
2.3-2.350.3171310.26692669X-RAY DIFFRACTION100
2.35-2.410.29981330.25562706X-RAY DIFFRACTION99.96
2.41-2.470.29371200.25382696X-RAY DIFFRACTION100
2.47-2.550.26411390.25142686X-RAY DIFFRACTION100
2.55-2.630.3131280.2532690X-RAY DIFFRACTION100
2.63-2.720.30141290.27992704X-RAY DIFFRACTION100
2.72-2.830.29791320.24842704X-RAY DIFFRACTION100
2.83-2.960.28481410.21932708X-RAY DIFFRACTION100
2.96-3.120.23951480.21852690X-RAY DIFFRACTION100
3.12-3.310.26761380.23392718X-RAY DIFFRACTION99.96
3.31-3.570.24281540.20552734X-RAY DIFFRACTION100
3.57-3.920.23541450.17552742X-RAY DIFFRACTION100
3.92-4.490.18651430.16872766X-RAY DIFFRACTION100
4.49-5.660.21351580.1772775X-RAY DIFFRACTION99.97
5.66-53.850.20491650.20232948X-RAY DIFFRACTION99.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.45767763245-1.91872593412-0.7359043297375.832484912470.1174596743510.85941543897-0.3566952684810.345540696419-0.675716140249-0.403758048151-0.265883660684-0.1361068514871.053417308010.2289347580940.4523217048050.9982548588380.2623686205560.3229596744670.683706349016-0.01091676024340.7788556941827.5866982965-24.17774527412.8379137429
27.27727580582-1.047085221571.348771008044.51585578882-1.654379484376.233064208530.1873662238420.289225223614-0.0988491734467-0.662227419895-0.295760395066-0.7294076577680.7617619510131.151895608770.05101550205620.5352408241720.263455376760.1211713939980.880503118490.1172206817440.64591771308633.3141876304-4.724399313821.07393083429
32.86009250043-0.310910835174-1.70645257191.63880852251-0.1129533009665.435772702940.4160281219240.1324584734480.458968577040.220598320327-0.0177367342695-0.0258138516627-0.7779658204510.266732185715-0.3425003453340.498030100302-0.002424616396880.1072680415080.3724549000130.1107633013010.59610304628717.750015057210.054245933315.8668155647
44.12873302596-0.307307638987-1.246686866252.68755053964-0.2985953538873.87498682253-0.1761710429470.355383813913-0.5781261461120.09075006468950.03132152917810.3312353281490.679620191018-0.6224153524330.1025204063240.496907572385-0.07918814273370.05871327306030.4183417359220.01808492673440.4795282599962.93356781551-13.792605746518.9975964969
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: C

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 291 through 405 )291 - 4051 - 115
22chain 'B' and (resid 406 through 486 )406 - 486116 - 145
33chain 'B' and (resid 487 through 629 )487 - 629146 - 288
44chain 'B' and (resid 630 through 871 )630 - 871289 - 530

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