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- PDB-5c46: Crystal structure of an engineered construct of phosphatidylinosi... -

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Basic information

Entry
Database: PDB / ID: 5c46
TitleCrystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in complex with GTP gamma S 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 / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / establishment of vesicle localization / exosomal secretion / rough endoplasmic reticulum membrane / amyloid-beta clearance by transcytosis / regulation of cilium assembly / regulation of protein transport / presynaptic endosome / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / protein transmembrane transport / Synthesis of PIPs at the Golgi membrane / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / melanosome transport / multivesicular body assembly / phosphatidylinositol biosynthetic process / protein localization to cilium / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / TBC/RABGAPs / protein localization to cell surface / syntaxin binding / dynein light intermediate chain binding / lysosome organization / mitotic metaphase chromosome alignment / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / exocytosis / inner ear development / cleavage furrow / positive regulation of epithelial cell migration / mitotic spindle assembly / positive regulation of G2/M transition of mitotic cell cycle / transport vesicle / phagocytic vesicle / vesicle-mediated transport / 14-3-3 protein binding / multivesicular body / centriole / receptor-mediated endocytosis / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network membrane / small monomeric GTPase / regulation of cytokinesis / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / regulation of long-term neuronal synaptic plasticity / recycling endosome / Schaffer collateral - CA1 synapse / recycling endosome membrane / neuron projection development / spindle pole / endocytic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / synaptic vesicle membrane / G protein activity / cytoplasmic vesicle / microtubule binding / 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 / cytoplasm / cytosol
Similarity search - Function
: / PI4KB/PIK1, accessory (PIK) domain / : / Small GTPase Rab domain 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 Rab domain 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / 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: 2.65 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 17, 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
E: Phosphatidylinositol 4-kinase beta
F: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1316
Polymers85,3762
Non-polymers7564
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-56 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.940, 97.950, 190.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules EF

#1: Protein Phosphatidylinositol 4-kinase beta / PtdIns 4-kinase beta / NPIK


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
#2: 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

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.99 %
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: 2.65→48.98 Å / Num. obs: 27529 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 61.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.047 / Net I/σ(I): 12.2 / Num. measured all: 173010 / Scaling rejects: 1209
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.65-2.786.20.922.62208835810.8150.40599.9
8.79-48.985.30.04341.645678610.9980.0298.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4d0l


Resolution: 2.65→48.975 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1402 5.13 %
Rwork0.2161 25912 -
obs0.2177 27314 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.59 Å2 / Biso mean: 82.1371 Å2 / Biso min: 38.95 Å2
Refinement stepCycle: final / Resolution: 2.65→48.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5172 0 43 4 5219
Biso mean--88.76 64.99 -
Num. residues----644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035319
X-RAY DIFFRACTIONf_angle_d0.5517190
X-RAY DIFFRACTIONf_chiral_restr0.021809
X-RAY DIFFRACTIONf_plane_restr0.002905
X-RAY DIFFRACTIONf_dihedral_angle_d10.3261979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6501-2.74480.44571230.39192559268299
2.7448-2.85470.37851150.32542554266999
2.8547-2.98460.31491270.28122530265799
2.9846-3.1420.34531340.2632558269299
3.142-3.33880.30291610.254725442705100
3.3388-3.59650.24081560.23792550270699
3.5965-3.95830.26231310.20842591272299
3.9583-4.53070.19831360.177226272763100
4.5307-5.70680.21511520.18626242776100
5.7068-48.98340.21531670.191927752942100
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)
10.97980.2180.65651.51642.2765.47660.1848-0.0467-0.26220.3431-0.0179-0.16480.5603-0.0583-0.16110.62430.0021-0.09630.4987-0.01240.5868-18.2248-0.3384-15.9611
23.71140.79480.32363.1339-0.83682.89380.12050.094-0.1797-0.0084-0.04860.36640.1724-0.4874-0.09410.5733-0.1169-0.02990.7105-0.24310.6624-31.0555-3.9675-35.591
32.2963-1.14910.97473.2165-0.89642.7784-0.01340.43060.1149-0.18830.0289-0.24550.04650.1839-0.03650.3817-0.08540.0090.5105-0.04360.4296-18.50622.4512-30.4254
43.2841.2497-0.66133.3180.0555.55940.1242-0.17820.05590.12720.11770.3523-0.0349-0.3936-0.26570.5255-0.0354-0.04770.79050.0820.5483-15.20458.117829.8523
52.01560.0742.60554.24780.11933.6185-1.0631-0.41511.63080.38710.84070.1995-0.74630.59350.09590.65030.12550.02990.8982-0.02970.7708-11.511513.494716.822
69.5575-0.5181-3.57534.8240.14977.11260.29790.25220.29590.12360.14390.4521-0.7656-1.4013-0.37810.64360.1002-0.05510.8970.10090.5744-16.823310.516434.5112
73.1064-1.52123.76834.7178-2.13144.58390.61980.42-0.4535-0.11870.0912-0.59790.44320.0377-0.61310.80290.1691-0.02231.1325-0.28611.47930.3472.010223.4024
83.4440.999-0.53583.63150.95023.71740.0965-0.6275-0.2753-0.51070.2468-0.15440.6054-0.4868-0.34250.8658-0.1232-0.00840.6440.17380.6256-11.363-0.285725.7541
98.33830.11512.08857.9721-1.04885.49870.147-1.0795-2.37260.32860.7964-1.26091.5183-0.4115-0.72480.974-0.005-0.05790.33210.21711.0582-8.4002-8.379522.8541
105.4462.1593-3.54895.49050.89513.5896-0.2433-0.4494-0.77720.9731-0.1439-0.00930.2193-0.62360.22280.8697-0.2319-0.11710.61870.22190.7799-15.5085-4.047630.0914
114.16862.78681.63812.28051.24426.00660.35740.1224-0.4497-0.3510.0840.17231.3465-1.6469-0.42490.9407-0.3448-0.10610.73950.09830.6684-21.9292-1.21469.072
125.8220.746-0.74175.8001-0.80656.2921-0.0147-0.4842-0.83360.4012-0.01440.16311.3779-1.7249-0.03950.8618-0.3928-0.06730.95590.13070.6497-22.7575-4.967420.7457
136.27071.7083-1.89945.275-2.23589.1665-0.0874-1.0263-0.69270.2791-0.10960.18650.3962-1.0218-0.05830.5834-0.09380.03661.33940.06270.6391-23.2251.123836.7053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 128 through 360 )E0
2X-RAY DIFFRACTION2chain 'E' and (resid 361 through 554 )E0
3X-RAY DIFFRACTION3chain 'E' and (resid 555 through 782 )E0
4X-RAY DIFFRACTION4chain 'F' and (resid 6 through 32 )F0
5X-RAY DIFFRACTION5chain 'F' and (resid 33 through 45 )F0
6X-RAY DIFFRACTION6chain 'F' and (resid 46 through 67 )F0
7X-RAY DIFFRACTION7chain 'F' and (resid 68 through 78 )F0
8X-RAY DIFFRACTION8chain 'F' and (resid 79 through 95 )F0
9X-RAY DIFFRACTION9chain 'F' and (resid 96 through 112 )F0
10X-RAY DIFFRACTION10chain 'F' and (resid 113 through 124 )F0
11X-RAY DIFFRACTION11chain 'F' and (resid 125 through 135 )F0
12X-RAY DIFFRACTION12chain 'F' and (resid 136 through 160 )F0
13X-RAY DIFFRACTION13chain 'F' and (resid 161 through 180 )F0

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