[English] 日本語
Yorodumi
- PDB-2x6k: THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x6k
TitleTHE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH PI-103
ComponentsPHOSPHOTIDYLINOSITOL 3 KINASE 59F
KeywordsTRANSFERASE / PI103 / PI-103 / AUTOPHAGY / PI3K CLASS III / PHOSPHOINOSITIDE 3-KINASE CLASS III
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
Chem-X6K / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)158,5167
Polymers157,5312
Non-polymers9855
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-65.9 kcal/mol
Surface area50860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.440, 155.680, 244.000
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
1416A706 - 769
2416B706 - 769
1516A786 - 804
2516B786 - 804
1616A833 - 949
2616B833 - 949

NCS oper: (Code: given
Matrix: (-0.007605, -0.1132, -0.9935), (0.001212, -0.9936, -0.1132), (-1, -0.000343, 0.007693)
Vector: 69.65, 109.4, 63.2)

-
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-X6K / 3-(4-MORPHOLIN-4-YLPYRIDO[3',2':4,5]FURO[3,2-D]PYRIMIDIN-2-YL)PHENOL / PI-103


Mass: 348.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16N4O3
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 455 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLY 455 TO ALA

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.17 Å3/Da / Density % sol: 70.25 % / 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 0.5MM PI-103 IN MOTHER LIQUOR.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.87→77.84 Å / Num. obs: 27069 / % possible obs: 99.7 % / Observed criterion σ(I): 1.3 / Redundancy: 3.56 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.46
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.33 / % possible all: 100

-
Processing

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

2x6h


Resolution: 3.5→61.74 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.875 / SU B: 76.068 / SU ML: 0.536 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.626 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1340 5 %RANDOM
Rwork0.235 ---
obs0.238 25729 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.26 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å20 Å2
2--2.13 Å20 Å2
3----5.32 Å2
Refinement stepCycle: LAST / Resolution: 3.5→61.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8995 0 67 0 9062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229286
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.661.97212581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg25.1827.7332415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73923.796432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.104151662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9181554
X-RAY DIFFRACTIONr_chiral_restr0.1030.21393
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216942
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.280.25224
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.26406
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.720.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4680.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8941.55511
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44828941
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.95333775
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.724.53640
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: 2788 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.675
2Bloose thermal3.5310
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 95 -
Rwork0.329 1890 -
obs--99.85 %
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)
10.45331.01260.35693.15040.88810.29390.0417-0.28740.12530.1426-0.1750.39240.064-0.16890.13330.37350.00470.05390.49070.09290.246515.373957.517646.0646
20.94421.93450.90754.22611.86311.0538-0.1152-0.0573-0.0469-0.4510.0505-0.2002-0.16890.03070.06460.3084-0.06160.08950.1725-0.01590.200725.620256.949434.8978
30.60790.52060.38391.35261.11211.521-0.10170.134-0.0475-0.16750.281-0.1648-0.06710.3491-0.17920.20890.05170.07160.21840.05670.205233.43857.85828.0252
40.3593-0.04790.47621.11170.4291.21-0.14770.0326-0.01-0.21530.2576-0.0379-0.05320.2343-0.10990.2774-0.08880.04550.3753-0.05920.155933.838856.987528.9148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A291 - 422
2X-RAY DIFFRACTION1B291 - 422
3X-RAY DIFFRACTION2A531 - 586
4X-RAY DIFFRACTION2B531 - 586
5X-RAY DIFFRACTION3A587 - 748
6X-RAY DIFFRACTION3B587 - 748
7X-RAY DIFFRACTION4A749 - 948
8X-RAY DIFFRACTION4B749 - 949

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more