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- PDB-9e4v: The structure of human vacuolar protein sorting 34 catalytic doma... -

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Basic information

Entry
Database: PDB / ID: 9e4v
TitleThe structure of human vacuolar protein sorting 34 catalytic domain bound to MES
ComponentsPhosphatidylinositol 3-kinase catalytic subunit type 3
KeywordsTRANSFERASE / Phosphatidylinositol 3-phosphate / Lipid regulator / autophagy / membrane trafficking / endocytosis / enzyme
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / postsynaptic endosome / 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 / positive regulation of protein lipidation / positive regulation by host of viral genome replication ...Toll Like Receptor 9 (TLR9) Cascade / postsynaptic endosome / 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 / positive regulation of protein lipidation / 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 / 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 / synaptic vesicle endocytosis / PI3K Cascade / axoneme / autophagosome assembly / RHO GTPases Activate NADPH Oxidases / autophagosome maturation / regulation of macroautophagy / cellular response to glucose starvation / autophagosome / regulation of cytokinesis / GABA-ergic synapse / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / autophagy / phagocytic vesicle membrane / endocytosis / late endosome / peroxisome / 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 / cytosol / cytoplasm
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
: / DI(HYDROXYETHYL)ETHER / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsAbiodun, W.O. / Fullmer, A. / Tsubaki, E. / Doukov, T. / 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. / Fullmer, A. / Singleton, J.D. / Tsubaki, E. / Cartwright, J. / Litchfield, C. / Doukov, T. / Peterson, M.A. / Moody, J.D.
History
DepositionOct 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: 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)69,39316
Polymers68,1501
Non-polymers1,24315
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.088, 114.088, 145.397
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 , 8 types, 106 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.47 Å3/Da / Density % sol: 64.53 % / Description: Rhombohedral
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 100mM MES, pH 6.0, 18% PEG3350

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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 11, 2023 / Details: Rh coated collimating mirror, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal monochromator, 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: 2.36→61.31 Å / Num. obs: 40128 / % possible obs: 99.96 % / Redundancy: 26.9 % / Biso Wilson estimate: 53.38 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2051 / Rpim(I) all: 0.04011 / Rrim(I) all: 0.209 / Net I/σ(I): 15.27
Reflection shellResolution: 2.36→2.444 Å / Redundancy: 26.4 % / Rmerge(I) obs: 3.989 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3953 / CC1/2: 0.457 / CC star: 0.792 / Rpim(I) all: 0.7858 / Rrim(I) all: 4.067 / % possible all: 99.95

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→61.31 Å / SU ML: 0.3101 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.195
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 2065 5.13 %
Rwork0.1985 38211 -
obs0.2002 40128 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.49 Å2
Refinement stepCycle: LAST / Resolution: 2.36→61.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4127 0 65 91 4283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784288
X-RAY DIFFRACTIONf_angle_d0.97275794
X-RAY DIFFRACTIONf_chiral_restr0.0549657
X-RAY DIFFRACTIONf_plane_restr0.0117735
X-RAY DIFFRACTIONf_dihedral_angle_d13.95361608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.410.35761370.30322500X-RAY DIFFRACTION99.96
2.41-2.470.32931480.2952483X-RAY DIFFRACTION100
2.47-2.540.33091480.26462506X-RAY DIFFRACTION99.96
2.54-2.610.25361340.24712498X-RAY DIFFRACTION100
2.61-2.70.24951290.24372505X-RAY DIFFRACTION100
2.7-2.790.26481130.24952557X-RAY DIFFRACTION100
2.79-2.910.30221300.23962513X-RAY DIFFRACTION100
2.91-3.040.25181540.21462507X-RAY DIFFRACTION100
3.04-3.20.21451300.19432535X-RAY DIFFRACTION100
3.2-3.40.24591340.19552547X-RAY DIFFRACTION100
3.4-3.660.22841430.19232531X-RAY DIFFRACTION99.96
3.66-4.030.17341400.16742572X-RAY DIFFRACTION100
4.03-4.610.19591220.1552591X-RAY DIFFRACTION100
4.61-5.810.24451530.18522611X-RAY DIFFRACTION100
5.81-61.310.21641500.20692755X-RAY DIFFRACTION99.76
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)
11.82368073271-0.556488700281-1.359373200184.45733289770.1866728480192.03696899933-0.1338488811860.10004169087-0.321878321236-0.276205727047-0.125979343493-0.244756588480.6519349649780.4816620674340.1896416781020.5620816320740.2310319323720.0628246477670.5737124224350.05843489355920.48232078177528.6980664039-15.46177230054.93871265794
21.76402583886-0.55867625277-1.282676509610.449865455302-0.3254530649434.690905205880.2982530700080.03686853238380.4172232094920.222938774687-0.0713164645523-0.000235225246061-1.000447048250.0635013686324-0.2694460392070.6283959965310.01351510140220.1393779567260.3066077051040.08903808442430.52857344269212.019674000914.836603868418.0465070635
33.48759705162-0.413257979529-1.175334775351.59121617531-0.1363463407852.75118456143-0.09002869065670.147024876605-0.5262312336730.0407007778106-0.04709476915940.2095174688680.57823341775-0.4326625938790.1142954740390.461696303302-0.0545841270790.03421186562150.3385397941980.01636804563070.3972235097492.68739278381-13.475817041518.9827676731
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 291 through 532 )291 - 5321 - 190
22chain 'B' and (resid 533 through 629 )533 - 629191 - 287
33chain 'B' and (resid 630 through 870 )630 - 870288 - 528

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