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- PDB-2x6f: THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS3... -

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Basic information

Entry
Database: PDB / ID: 2x6f
TitleTHE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH 3-METHYLADENINE
ComponentsPHOSPHOTIDYLINOSITOL 3 KINASE 59F
KeywordsTRANSFERASE
Function / homology
Function and homology information


positive regulation of nurse cell apoptotic process / omegasome / Synthesis of PIPs at the Golgi membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / larval midgut cell programmed cell death / Macroautophagy / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I ...positive regulation of nurse cell apoptotic process / omegasome / Synthesis of PIPs at the Golgi membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / larval midgut cell programmed cell death / Macroautophagy / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / epithelial structure maintenance / protein targeting to lysosome / pexophagy / phagophore assembly site / phosphatidylinositol-3-phosphate biosynthetic process / phosphatidylinositol 3-kinase / 1-phosphatidylinositol-3-kinase activity / regulation of early endosome to late endosome transport / neuron remodeling / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / establishment or maintenance of cell polarity / autophagosome membrane / autophagosome assembly / phagocytosis / cellular response to starvation / macroautophagy / endocytosis / peroxisome / early endosome / endosome / ATP binding / membrane / cytoplasm
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
6-AMINO-3-METHYLPURINE / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMiller, S. / Tavshanjian, B. / Oleksy, A. / Perisic, O. / Houseman, B.T. / Shokat, K.M. / Williams, R.L.
CitationJournal: Science / Year: 2010
Title: Shaping Development of Autophagy Inhibitors with the Structure of the Lipid Kinase Vps34.
Authors: Miller, S. / Tavshanjian, B. / Oleksy, A. / Perisic, O. / Houseman, B.T. / Shokat, K.M. / Williams, R.L.
History
DepositionFeb 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOTIDYLINOSITOL 3 KINASE 59F
B: PHOSPHOTIDYLINOSITOL 3 KINASE 59F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,8314
Polymers157,5312
Non-polymers3002
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-21.3 kcal/mol
Surface area50820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.070, 155.140, 244.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A329 - 565
2116B329 - 565
1216A606 - 619
2216B606 - 619
1316A631 - 634
2316B631 - 634
1416A672 - 698
2416B672 - 698
1516A706 - 769
2516B706 - 769
1616A786 - 804
2616B786 - 804
1716A833 - 949
2716B833 - 949

NCS oper: (Code: given
Matrix: (-0.007953, -0.1179, -0.993), (6.8E-5, -0.993, 0.1179), (-1, 0.00087, 0.007905)
Vector: 70.15, 108.7, 63.7)

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Components

#1: Protein PHOSPHOTIDYLINOSITOL 3 KINASE 59F / GH13170P / VPS34


Mass: 78765.469 Da / Num. of mol.: 2 / Fragment: HELICAL DOMAIN, KINASE DOMAIN RESIDUES 258-949 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 RIPL
References: UniProt: Q9W1M7, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, phosphatidylinositol-4-phosphate 3-kinase
#2: Chemical ChemComp-3MA / 6-AMINO-3-METHYLPURINE


Mass: 150.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N5

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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: 4.26 Å3/Da / Density % sol: 70.92 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLISED IN 0.88M AMMONIUM SULPHATE, 100MM DI-POTASSIUM HYDROGEN PHOSPHATE AND 100MM DI-SODIUM HYDROGEN PHOSPHATE (TITRATED TO PH 7.5 WITH ORTHOPHOSPHORIC ACID). PROTEIN WAS ...Details: PROTEIN WAS CRYSTALLISED IN 0.88M AMMONIUM SULPHATE, 100MM DI-POTASSIUM HYDROGEN PHOSPHATE AND 100MM DI-SODIUM HYDROGEN PHOSPHATE (TITRATED TO PH 7.5 WITH ORTHOPHOSPHORIC ACID). PROTEIN WAS SOAKED WITH 1MM 3-MA IN MOTHER LIQUOR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9743
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9743 Å / Relative weight: 1
ReflectionResolution: 3.3→72.92 Å / Num. obs: 31665 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.99
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.66 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.04 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X6H

2x6h


Resolution: 3.3→61.13 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 62.715 / SU ML: 0.471 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.54 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1564 4.9 %RANDOM
Rwork0.242 ---
obs0.245 30097 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å20 Å2
2--2.09 Å20 Å2
3----5.03 Å2
Refinement stepCycle: LAST / Resolution: 3.3→61.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8875 0 22 0 8897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229116
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.96612346
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg25.4747.7512399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72723.803426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.413151636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0641552
X-RAY DIFFRACTIONr_chiral_restr0.10.21375
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216816
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.30.25232
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.26363
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4730.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4440.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2011.55434
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81528814
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.04233682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8594.53532
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 2965 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.65
2Bloose positional0.65
1Aloose thermal6.510
2Bloose thermal6.510
LS refinement shellResolution: 3.3→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 126 -
Rwork0.334 2204 -
obs--99.19 %
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)
1-0.85471.7312-0.38073.82.0518-1.5030.3668-0.50980.33010.1943-0.74880.19030.29-0.16040.3820.8385-0.22280.01680.9153-0.13850.653313.538957.119948.7423
20.52751.4250.43663.78041.16990.62160.0344-0.30380.0968-0.0312-0.19840.2599-0.0107-0.1210.1640.19190.0684-0.05540.2430.0980.225117.06957.484444.3388
31.08931.88420.93263.35631.7681.0893-0.17650.11010.0847-0.22830.22480.1022-0.1080.1395-0.04820.1361-0.091-0.01470.09120.04050.162823.646656.865737.3306
40.66320.76550.4941.65351.22041.2126-0.06630.0201-0.0544-0.12960.2006-0.15-0.06820.3117-0.13430.0823-0.01960.03060.16340.03380.119733.007557.588628.7439
5-0.05840.15430.76740.93320.69711.335-0.08970.08040.007-0.22350.2498-0.07770.09130.2757-0.16010.2102-0.08960.07970.4288-0.08950.211134.195856.76328.9625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A291 - 344
2X-RAY DIFFRACTION1B291 - 344
3X-RAY DIFFRACTION2A345 - 421
4X-RAY DIFFRACTION2B345 - 421
5X-RAY DIFFRACTION3A532 - 561
6X-RAY DIFFRACTION3B532 - 560
7X-RAY DIFFRACTION4A568 - 748
8X-RAY DIFFRACTION4B568 - 748
9X-RAY DIFFRACTION5A749 - 948
10X-RAY DIFFRACTION5B749 - 949

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