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- PDB-11mm: The structure of human Vacuolar Protein Sorting 34 catalytic doma... -

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Basic information

Entry
Database: PDB / ID: 11mm
TitleThe structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-81
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 / 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 / response to L-leucine / protein localization to phagophore assembly site / 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 / regulation of macroautophagy / RHO GTPases Activate NADPH Oxidases / 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
: / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsAbiodun, W.O. / Litchfield, C.M. / Peterson, M.A. / 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-II-83
Authors: Abiodun, W.O. / Litchfield, C.M. / Burtch, M. / Cartwright, J. / Dass, R. / Singleton, J.D. / Doukov, T. / Peterson, M.A. / Moody, J.D.
History
DepositionMar 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 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)68,7075
Polymers68,1501
Non-polymers5574
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.448, 114.448, 145.847
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
11A-1021-

HOH

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Components

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1C9V / (8S)-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]pyrazolo[1,5-a]pyrimidine


Mass: 294.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.73, 1.85
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2024
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 wavelength
IDWavelength (Å)Relative weight
10.731
21.851
ReflectionResolution: 2.69→53.27 Å / Num. obs: 27560 / % possible obs: 99.88 % / Redundancy: 26.9 % / Biso Wilson estimate: 87.43 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.01673 / Rrim(I) all: 0.02366 / Net I/σ(I): 17.88
Reflection shellResolution: 2.69→2.786 Å / Redundancy: 28.3 % / Rmerge(I) obs: 4.455 / Mean I/σ(I) obs: 0.77 / Num. unique obs: 2688 / CC1/2: 0.477 / CC star: 0.804 / Rrim(I) all: 4.536 / % possible all: 99.3

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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: 2.69→53.27 Å / SU ML: 0.542 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2646 1329 4.82 %
Rwork0.2048 26254 -
obs0.2076 27560 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.46 Å2
Refinement stepCycle: LAST / Resolution: 2.69→53.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4240 0 34 21 4295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00454409
X-RAY DIFFRACTIONf_angle_d0.62215980
X-RAY DIFFRACTIONf_chiral_restr0.0386666
X-RAY DIFFRACTIONf_plane_restr0.0049777
X-RAY DIFFRACTIONf_dihedral_angle_d11.89121637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.80.48471390.40892841X-RAY DIFFRACTION99.33
2.8-2.920.37951430.33522855X-RAY DIFFRACTION99.9
2.92-3.080.37261670.2872860X-RAY DIFFRACTION99.97
3.08-3.270.3161480.27932884X-RAY DIFFRACTION100
3.27-3.520.33251340.24932892X-RAY DIFFRACTION100
3.52-3.880.28181420.2032914X-RAY DIFFRACTION99.97
3.88-4.440.23171510.1772917X-RAY DIFFRACTION100
4.44-5.590.2191520.17312961X-RAY DIFFRACTION100
5.59-53.270.24121530.18113130X-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)
17.85060503478-1.80088915896-1.18850090832.616090553811.866082711832.95718413295-0.260327600447-0.2377143576460.01376469400970.126489371014-0.01235797342550.717245144671-0.475560848808-0.7775178498180.2848475773540.6158709466540.169073163251-0.01530586221970.7941048320830.02998408566580.765556870252-26.316680610826.6033545795-2.18730307697
22.02538856991-2.804683786950.699506022756.665438732470.7380186041155.685858318090.1077954154880.6600757337830.961047947867-0.625270002894-0.12588884289-0.30709997227-1.241878184090.586202529040.08743009170741.11350476872-0.0276694507025-0.04269806166660.9375924844430.03921069997541.12211891763-0.61316592560436.3149924948-5.90480216159
31.98670441943-1.33312082779-1.342509443283.885642055752.39738703956.06113644084-0.02482323929250.2726757117470.192338429156-0.2090153681090.191856960122-0.292701523299-0.5834885466880.551803033796-0.1830997465330.48314232846-0.127207678233-0.01654167495020.655717629360.03171916386310.7145938180248.6735367375918.6119353689-14.5722440128
43.280796989110.992909767897-0.220601798425.893466039780.2139821764413.6955830022-0.267567213240.421890840905-0.432597674219-0.1727068599610.1374426840630.593845322520.552072407947-0.7011041638970.1195299464060.556412513986-0.1691204629220.04032872027730.7856992324-0.1049574397650.590691170247-13.78652333731.89801016526-19.0314229415
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 289 through 405 )289 - 4051 - 117
22chain 'A' and (resid 406 through 474 )406 - 474118 - 143
33chain 'A' and (resid 475 through 629 )475 - 629144 - 298
44chain 'A' and (resid 630 through 870 )630 - 870299 - 539

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