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- PDB-5c4g: Crystal structure of an engineered construct of phosphatidylinosi... -

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Basic information

Entry
Database: PDB / ID: 5c4g
TitleCrystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta with the inhibitor BQR695 in complex with GDP loaded Rab11
Components
  • Phosphatidylinositol 4-kinase beta
  • Ras-related protein Rab-11A
KeywordsTransferase/Signaling Protein / Protein-protein complex / 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 / Synthesis of PIPs at the Golgi membrane / neurotransmitter receptor transport, endosome to postsynaptic membrane / 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 / 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 / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / cleavage furrow / inner ear development / centriolar satellite / mitotic spindle assembly / vesicle-mediated transport / transport vesicle / phagocytic vesicle / 14-3-3 protein binding / 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 / trans-Golgi network membrane / regulation of cytokinesis / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / 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-BQR / GUANOSINE-5'-DIPHOSPHATE / 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
Natural Sciences and Engineering Research Council (NSERC, Canada)NSERC-2014-05218 Canada
CitationJournal: Protein Sci. / Year: 2016
Title: Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIII beta with Rab11.
Authors: Fowler, M.L. / McPhail, J.A. / Jenkins, M.L. / Masson, G.R. / Rutaganira, F.U. / Shokat, K.M. / Williams, R.L. / Burke, J.E.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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
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)86,3887
Polymers85,3762
Non-polymers1,0125
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-63 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.820, 105.400, 188.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules BE

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


Mass: 24691.818 Da / Num. of mol.: 1 / Mutation: Q70L
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, PIK4CB / Plasmid: pOPTH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase

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Non-polymers , 4 types, 5 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-BQR / N~2~-[7-(3,4-dimethoxyphenyl)quinoxalin-2-yl]-N-methylglycinamide


Mass: 352.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O3

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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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / 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→54.04 Å / Num. obs: 16111 / % possible obs: 95.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 89.67 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.1
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.9 / % possible all: 91.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D0L

4d0l


Resolution: 3.2→54.04 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 841 5.27 %
Rwork0.254 --
obs0.255 15969 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.6 Å2
Refinement stepCycle: LAST / Resolution: 3.2→54.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 65 0 4800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025163
X-RAY DIFFRACTIONf_angle_d0.4156980
X-RAY DIFFRACTIONf_dihedral_angle_d8.9361912
X-RAY DIFFRACTIONf_chiral_restr0.016783
X-RAY DIFFRACTIONf_plane_restr0.002876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.40050.39321310.38262340X-RAY DIFFRACTION90
3.4005-3.6630.34081360.32642357X-RAY DIFFRACTION91
3.663-4.03150.29321330.26652481X-RAY DIFFRACTION95
4.0315-4.61460.30091540.2422516X-RAY DIFFRACTION96
4.6146-5.81290.2421310.24042628X-RAY DIFFRACTION98
5.8129-54.05240.26971560.22212806X-RAY DIFFRACTION100
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)
10.07890.1218-0.10410.1995-0.20410.2205-0.3548-0.38180.3806-0.41940.78780.77670.60330.70140.00131.23660.0068-0.05581.6220.24040.89-14.88826.472723.93
20.281-0.5629-0.54191.12281.08341.04680.1453-0.83240.2555-0.08350.7961-0.10420.15020.69870.2930.98080.1215-0.23411.75020.26820.9111-12.16463.577629.6764
31.27160.24711.46610.04790.28521.6908-0.5582-0.34480.1268-0.2494-0.28170.3435-0.13250.1065-0.58751.93320.1801-0.29071.2620.42430.8642-15.6752-3.807214.5973
40.33510.70220.06511.47550.14010.01350.08510.4832-0.4951-0.14640.9535-1.47240.8870.30260.15451.24370.4356-0.1321.6920.48031.4589-8.9053-11.412516.6648
51.67540.21421.45980.7069-0.40641.78450.1993-0.69141.37370.26580.14990.46840.1648-0.0545-0.00881.13790.0854-0.21221.46580.31910.7564-15.6944-7.723125.4835
60.24060.25230.07610.25880.07870.0230.12960.01090.01380.16720.38070.31730.204-0.0347-01.4618-0.1158-0.12081.12220.29810.8593-23.2029-6.863410.1156
70.049-0.319-0.03653.6144-0.66030.51680.2786-0.69010.1703-1.0206-0.4394-0.39860.3526-0.83290.01030.864-0.0696-0.1291.51180.32190.8519-23.2133-0.97323.2653
80.24750.44240.02010.73390.02020.5844-0.06950.0870.07090.16920.11580.17840.10830.176800.92890.174-0.05570.71120.00420.6709-17.9286.3862-8.748
90.90520.53080.84450.96860.54510.7771-0.04420.2923-0.11140.18690.00350.1040.0156-0.00280.00730.3940.0146-0.02140.7489-0.2610.7086-28.3494-0.0294-39.865
100.3038-0.03820.14241.117-0.04270.0512-0.22250.1447-0.17730.08710.15690.0621-0.23220.18390.00010.763-0.0972-0.08830.51230.04360.6129-20.153625.4729-30.8991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 7 THROUGH 39 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 40 THROUGH 85 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 86 THROUGH 95 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 96 THROUGH 112 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 113 THROUGH 124 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 125 THROUGH 145 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 146 THROUGH 173 )
8X-RAY DIFFRACTION8CHAIN 'E' AND (RESID 128 THROUGH 307 )
9X-RAY DIFFRACTION9CHAIN 'E' AND (RESID 308 THROUGH 531 )
10X-RAY DIFFRACTION10CHAIN 'E' AND (RESID 532 THROUGH 782 )

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