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- PDB-5anl: Crystal structure of VPS34 in complex with (2S)-8-((3R)-3- Methyl... -

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Basic information

Entry
Database: PDB / ID: 5anl
TitleCrystal structure of VPS34 in complex with (2S)-8-((3R)-3- Methylmorpholin-4-yl)-1-(3-methyl-2-oxo- butyl)-2-(trifluoromethyl)-3, 4-dihydro-2H-pyrimido(1,2-a)pyrimidin-6- one, processed with the CrystalDirect automated mounting and cryo-cooling technology
ComponentsPHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3
KeywordsTRANSFERASE / LIPID KINASE / AUTOMATED CRYSTAL HARVESTING / AUTOMATED CRYO- COOLING / CRYSTALDIRECT
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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Phosphatidylinositol 3-kinase, accessory domain (PIK) / 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 ...Phosphatidylinositol 3-kinase, Vps34 type / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Phosphatidylinositol 3-kinase, accessory domain (PIK) / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-RBQ / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsZander, U. / Hoffmann, G. / Mathieu, M. / Marquette, J.-P. / Cornaciu, I. / Cipriani, F. / Marquez, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: Automated Harvesting and Processing of Protein Crystals Through Laser Photoablation.
Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A.
History
DepositionSep 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9882
Polymers68,5971
Non-polymers3901
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.215, 145.763, 61.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 68597.391 Da / Num. of mol.: 1
Fragment: VPS34 HELICAL AND KINASE DOMAINS, UNP RESIDUES 282-879
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase
#2: Chemical ChemComp-RBQ / (8S)-2-(morpholin-4-yl)-9-[2-(propan-2-yloxy)ethyl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one


Mass: 390.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25F3N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.3 % / Description: NONE
Crystal growDetails: 0.1 M TRIS, PH=7.5, 1.8 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 22467 / % possible obs: 99.9 % / Observed criterion σ(I): 2.1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 16.111 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.62 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26667 1108 4.9 %RANDOM
Rwork0.20534 ---
obs0.20839 21323 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.423 Å2
Baniso -1Baniso -2Baniso -3
1-6.19 Å20 Å20 Å2
2---0.01 Å20 Å2
3----6.18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 27 85 4416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194416
X-RAY DIFFRACTIONr_bond_other_d0.0020.024236
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9815993
X-RAY DIFFRACTIONr_angle_other_deg0.81639735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65724.877203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52315776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7371524
X-RAY DIFFRACTIONr_chiral_restr0.0750.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02973
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9024.4372169
X-RAY DIFFRACTIONr_mcbond_other2.9014.4382170
X-RAY DIFFRACTIONr_mcangle_it4.5846.6542707
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3214.7742247
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 66 -
Rwork0.346 1550 -
obs--100 %

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