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

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Basic information

Entry
Database: PDB / ID: 11yc
TitleThe structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-123
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
: / DI(HYDROXYETHYL)ETHER / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsCartwright, J.J. / Abiodun, W.O. / 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-123
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 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: 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)68,7688
Polymers68,1501
Non-polymers6187
Water63135
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.253, 114.253, 146.029
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 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 / 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, 42 molecules

#2: Chemical ChemComp-A1DAY / (8S)-3-(6-butyl-1,3-benzothiazol-2-yl)pyrazolo[1,5-a]pyrimidine


Mass: 308.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.43 Å3/Da / Density % sol: 64.49 % / Description: Hexagonal
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: Ammonium Acetate, HEPES, Polyethylene glycol 3,350

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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 EIGER2 XE 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: 2.41→57.13 Å / Num. obs: 37632 / % possible obs: 99.87 % / Redundancy: 21.9 % / Biso Wilson estimate: 69.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07572 / Rpim(I) all: 0.01581 / Rrim(I) all: 0.07745 / Net I/σ(I): 25.27
Reflection shellResolution: 2.41→2.496 Å / Redundancy: 8.7 % / Rmerge(I) obs: 2.685 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 3687 / CC1/2: 0.226 / Rpim(I) all: 0.9364 / Rrim(I) all: 2.856 / % possible all: 99.01

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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: 2.41→57.13 Å / SU ML: 0.384 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1426
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2195 1812 4.77 %
Rwork0.1938 36198 -
obs0.195 37632 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.05 Å2
Refinement stepCycle: LAST / Resolution: 2.41→57.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4253 0 33 35 4321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324389
X-RAY DIFFRACTIONf_angle_d0.54295940
X-RAY DIFFRACTIONf_chiral_restr0.0389666
X-RAY DIFFRACTIONf_plane_restr0.0039764
X-RAY DIFFRACTIONf_dihedral_angle_d13.11811647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.470.41551560.33412692X-RAY DIFFRACTION98.68
2.47-2.550.28511540.28252691X-RAY DIFFRACTION99.93
2.55-2.630.29681610.27082710X-RAY DIFFRACTION100
2.63-2.720.35711350.29142767X-RAY DIFFRACTION100
2.72-2.830.3641460.27222733X-RAY DIFFRACTION100
2.83-2.960.27891180.24142772X-RAY DIFFRACTION100
2.96-3.120.27841340.22872776X-RAY DIFFRACTION100
3.12-3.310.2411290.23652778X-RAY DIFFRACTION100
3.31-3.570.23171550.22232765X-RAY DIFFRACTION100
3.57-3.930.20671210.18132813X-RAY DIFFRACTION100
3.93-4.490.17031270.15832819X-RAY DIFFRACTION100
4.49-5.660.18271300.15912870X-RAY DIFFRACTION100
5.66-57.130.19321460.17353012X-RAY DIFFRACTION99.81
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)
16.478439383081.099202461330.06172549514783.03977924865-1.267722293963.95416241166-0.2620824865130.4744309830550.400225765069-0.09492330069480.0171454868438-0.228922928136-0.7863172467710.6801821998820.1832211223680.655870424072-0.210735810101-0.07829172626970.574492011914-0.003361182734290.51069894268513.588166751129.1345926757-33.8586061217
21.91980072371.09841941171-0.7185213172452.554740311-1.867098590725.30220328955-0.0518242422094-0.2627990143660.148429023250.1979919581730.2817487044030.236093725584-0.490550523838-0.52182137765-0.2685333702120.3842048393310.118546277376-0.003639195787080.4528979424710.0045299462610.545263108364-9.0847711763718.6500573929-21.7161988769
32.51937840447-0.0175899224906-0.03233110145284.97224948837-0.4684551700523.41040265839-0.267475015006-0.217708616703-0.3564718234710.1839399599860.157802339104-0.4822970415480.4779446615610.6480841685450.1024935062160.4619114967550.1400032639760.02925765132270.6008292835620.02990265203640.49687608041913.66987544491.88009756973-17.4692641097
46.474361243550.2768962157510.8230000516164.00325163741-1.281985866232.72335538130.007492718411120.3526378546440.1489636557660.371333106544-0.277325943912-1.15459736383-0.2180897665251.026682704550.2340462265940.656560321036-0.323268936398-0.02838005657871.105609749760.1043847248770.91171980593435.059062203426.5133466468-33.769110126
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 342 through 474 )342 - 47453 - 140
22chain 'B' and (resid 475 through 629 )475 - 629141 - 295
33chain 'B' and (resid 630 through 871 )630 - 871296 - 537
44chain 'B' and (resid 290 through 341 )290 - 3411 - 52

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