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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 endocytic recycling / early endosome to recycling endosome transport / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / postsynaptic recycling endosome ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of endocytic recycling / early endosome to recycling endosome transport / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / regulation of cilium assembly / exosomal secretion / rough endoplasmic reticulum membrane / amyloid-beta clearance by transcytosis / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / melanosome transport / VxPx cargo-targeting to cilium / protein transmembrane transport / Synthesis of PIPs at the Golgi membrane / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / Golgi to plasma membrane protein transport / phosphatidylinositol biosynthetic process / multivesicular body assembly / protein localization to cilium / establishment of protein localization to membrane / syntaxin binding / protein localization to cell surface / TBC/RABGAPs / dynein light intermediate chain binding / lysosome organization / mitotic metaphase chromosome alignment / phosphatidylinositol-mediated signaling / exocytosis / phosphatidylinositol phosphate biosynthetic process / inner ear development / cleavage furrow / positive regulation of epithelial cell migration / mitotic spindle assembly / transport vesicle / vesicle-mediated transport / phagocytic vesicle / positive regulation of G2/M transition of mitotic cell cycle / 14-3-3 protein binding / multivesicular body / centriole / receptor-mediated endocytosis / cytoplasmic vesicle membrane / Anchoring of the basal body to the plasma membrane / regulation of cytokinesis / small monomeric GTPase / trans-Golgi network membrane / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / recycling endosome / spindle pole / recycling endosome membrane / neuron projection development / Vasopressin regulates renal water homeostasis via Aquaporins / endocytic vesicle membrane / G protein activity / microtubule binding / cytoplasmic vesicle / vesicle / mitochondrial outer membrane / endosome / Golgi membrane / GTPase activity / centrosome / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / 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. ...: / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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

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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


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


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

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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: 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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