[English] 日本語
Yorodumi
- PDB-5euq: Crystal structure of an engineered construct of phosphatidylinosi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5euq
TitleCrystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta with a potent and selective inhibitor in complex with GDP loaded Rab11
Components
  • Phosphatidylinositol 4-kinase beta
  • Ras-related protein Rab-11A
KeywordsTransferase/Signaling Protein / lipid kinase / GTPase complex / Transferase-Signaling Protein complex
Function / homology
Function and homology information


regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / rough endoplasmic reticulum membrane / melanosome transport / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / protein localization to cilium / multivesicular body assembly / phosphatidylinositol biosynthetic process / dynein light intermediate chain binding / phosphatidylinositol-mediated signaling / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / lysosome organization / positive regulation of epithelial cell migration / exocytosis / inner ear development / cleavage furrow / phosphatidylinositol phosphate biosynthetic process / centriolar satellite / mitotic spindle assembly / phagocytic vesicle / transport vesicle / vesicle-mediated transport / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / multivesicular body / receptor-mediated endocytosis / small monomeric GTPase / G protein activity / 14-3-3 protein binding / trans-Golgi network membrane / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / mitochondrial outer membrane / endosome / phosphorylation / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / PI4KB/PIK1, accessory (PIK) domain / small GTPase Rab1 family profile. / 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 ...: / PI4KB/PIK1, accessory (PIK) domain / small GTPase Rab1 family profile. / 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 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5S8 / GUANOSINE-5'-DIPHOSPHATE / Phosphatidylinositol 4-kinase beta / Ras-related protein Rab-11A / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsBurke, J.E. / Fowler, M.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FRN 142393 Canada
CitationJournal: J.Med.Chem. / Year: 2016
Title: Design and Structural Characterization of Potent and Selective Inhibitors of Phosphatidylinositol 4 Kinase III beta.
Authors: Rutaganira, F.U. / Fowler, M.L. / McPhail, J.A. / Gelman, M.A. / Nguyen, K. / Xiong, A. / Dornan, G.L. / Tavshanjian, B. / Glenn, J.S. / Shokat, K.M. / Burke, J.E.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ras-related protein Rab-11A
E: Phosphatidylinositol 4-kinase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5016
Polymers85,3762
Non-polymers1,1254
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-45 kcal/mol
Surface area29220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.900, 103.490, 188.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 24691.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Plasmid: pOPTG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62491
#2: Protein Phosphatidylinositol 4-kinase beta / PtdIns 4-kinase beta / NPIK / PI4K92


Mass: 60683.840 Da / Num. of mol.: 1 / Mutation: S294A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KB / Plasmid: pOPTH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UBF8, UniProt: O02810, 1-phosphatidylinositol 4-kinase
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-5S8 / ~{N}-[5-[3-[[(4-hydroxyphenyl)amino]-bis(oxidanyl)-$l^{4}-sulfanyl]-4-methoxy-phenyl]-4-methyl-1,3-thiazol-2-yl]cyclopentanecarboxamide


Mass: 489.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N3O5S2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 5.6
Details: PEG-4000, sodium citrate, ammonium sulfate, glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→47.34 Å / Num. obs: 16316 / % possible obs: 98.63 % / Redundancy: 4.1 % / Biso Wilson estimate: 82.35 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.2-3.3140.70192.11199.44
9.05-48.93.60.03522.3196.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.3.11data scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4D0L

4d0l


Resolution: 3.2→47.34 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.29
RfactorNum. reflection% reflection
Rfree0.266 856 5.26 %
Rwork0.233 --
obs0.2359 16274 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 191.4 Å2 / Biso mean: 97.8217 Å2 / Biso min: 48.8 Å2
Refinement stepCycle: final / Resolution: 3.2→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 96 0 5066
Biso mean--116.95 --
Num. residues----619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035141
X-RAY DIFFRACTIONf_angle_d0.6136956
X-RAY DIFFRACTIONf_chiral_restr0.022780
X-RAY DIFFRACTIONf_plane_restr0.002871
X-RAY DIFFRACTIONf_dihedral_angle_d12.9811903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.40070.36041440.32252516266099
3.4007-3.66310.31031410.28082544268599
3.6631-4.03160.27311360.24442542267899
4.0316-4.61450.26631560.21352544270099
4.6145-5.81220.25231280.22362592272098
5.8122-47.34530.2311510.21362680283197
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)
1-0.0153-0.2390.00350.40910.17660.42130.07990.66910.24910.5681-0.2466-0.59370.4414-0.53240.00360.82250.02540.02651.532-0.19310.8989-230.4217211.626350.7576
20.1283-0.1678-0.01840.14010.0349-0.01860.14340.48290.32350.07830.35870.4038-0.8275-0.0547-0.00020.95210.176-0.14660.9703-0.05250.9124-231.4536220.2607361.0467
30.029-0.02450.04140.0039-0.03150.0159-0.17050.0428-0.23910.19510.2745-0.1386-0.2573-0.6754-0.00040.62120.0953-0.12491.4941-0.23860.7626-227.8914213.7059344.5441
4-0.05420.0083-0.00470.1064-0.08140.0036-0.04370.3720.09010.7694-0.23340.37620.6635-0.2831-01.0776-0.3234-0.19421.2506-0.14360.7867-235.1682204.2284354.9884
50.2652-0.3543-0.07480.24140.12220.0138-0.2439-0.23310.4124-0.0880.0081-0.18840.2437-0.8955-0.00080.8754-0.2721-0.09721.166-0.21860.634-233.8844197.4988356.869
60.0538-0.09150.06270.03340.0091-0.00320.1305-0.32910.76560.09220.4393-0.33130.3787-0.03170.00041.42070.2091-0.06540.9153-0.12330.8838-222.284206.2305371.1369
7-0.01130.0217-0.01640.00290.00130.02070.22140.01560.0824-0.40860.26190.11770.0049-0.23540.00011.88450.4064-0.34991.1319-0.39371.0535-222.0723193.1289360.7824
80.2451-0.051-0.06110.0204-0.07380.0912-0.00971.09790.07880.17040.10560.3994-0.08250.5491-0.00020.88730.14230.06491.626-0.00780.6264-221.3065207.1032359.8487
90.0911-0.0602-0.00690.00670.01240.01890.3370.6597-0.1689-0.5582-0.2562-0.72870.01480.5787-0.00030.98510.14910.02611.322-0.17850.7359-221.7994206.6344347.8768
100.22980.38690.0956-0.0626-0.13160.35920.095-0.2863-0.1872-0.2290.0832-0.08810.0316-0.1739-0.00010.8412-0.0968-0.05250.72070.01260.6554-226.2735218.9247381.878
110.44940.02950.05160.0239-0.75570.34410.0172-0.0755-0.2574-0.18170.0225-0.03030.1883-0.0162-0.00010.7348-0.1175-0.06020.50050.02680.7169-226.1561203.392404.0798
120.1366-0.0187-0.04510.35620.08560.53410.1164-0.220.0098-0.03750.08240.07210.02130.3724-00.46230.02830.00170.8560.1320.6973-211.0784206.789414.4359
13-0.09390.15330.15960.960.18010.7252-0.1055-0.1856-0.0635-0.1241-0.0147-0.0389-0.1443-0.0944-00.67220.029-0.0670.5898-0.04870.6229-225.3361231.7566408.6545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 7:32 )B7 - 32
2X-RAY DIFFRACTION2( CHAIN B AND RESID 33:46 )B33 - 46
3X-RAY DIFFRACTION3( CHAIN B AND RESID 47:66 )B47 - 66
4X-RAY DIFFRACTION4( CHAIN B AND RESID 67:95 )B67 - 95
5X-RAY DIFFRACTION5( CHAIN B AND RESID 96:124 )B96 - 124
6X-RAY DIFFRACTION6( CHAIN B AND RESID 125:135 )B125 - 135
7X-RAY DIFFRACTION7( CHAIN B AND RESID 136:146 )B136 - 146
8X-RAY DIFFRACTION8( CHAIN B AND RESID 147:160 )B147 - 160
9X-RAY DIFFRACTION9( CHAIN B AND RESID 161:173 )B161 - 173
10X-RAY DIFFRACTION10( CHAIN E AND RESID 128:185 )E128 - 185
11X-RAY DIFFRACTION11( CHAIN E AND RESID 186:347 )E186 - 347
12X-RAY DIFFRACTION12( CHAIN E AND RESID 348:540 )E348 - 540
13X-RAY DIFFRACTION13( CHAIN E AND RESID 541:782 )E541 - 782

+
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