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- PDB-5fbq: PI4KB in complex with Rab11 and the MI358 Inhibitor -

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Basic information

Entry
Database: PDB / ID: 5fbq
TitlePI4KB in complex with Rab11 and the MI358 Inhibitor
Components
  • Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta
  • Ras-related protein Rab-11A
KeywordsTRANSFERASE / Inhibitor / Complex / Kinase / Lipid
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 / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization ...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 / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / exosomal secretion / regulation of cilium assembly / melanosome transport / rough endoplasmic reticulum membrane / amyloid-beta clearance by transcytosis / astral microtubule organization / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein transmembrane transport / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / Golgi to plasma membrane protein transport / multivesicular body assembly / phosphatidylinositol biosynthetic process / protein localization to cilium / dynein light intermediate chain binding / establishment of protein localization to membrane / TBC/RABGAPs / protein localization to cell surface / syntaxin binding / mitotic metaphase chromosome alignment / lysosome organization / positive regulation of epithelial cell migration / exocytosis / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / cleavage furrow / inner ear development / centriolar satellite / mitotic spindle assembly / phagocytic vesicle / vesicle-mediated transport / 14-3-3 protein binding / transport vesicle / 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 / regulation of cytokinesis / trans-Golgi network membrane / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / G protein activity / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / mitochondrial outer membrane / endosome / 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- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site ...: / 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- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / 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-5W6 / 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 / Resolution: 3.789 Å
AuthorsChalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E.
CitationJournal: To Be Published
Title: PI4KB in complex with Rab11 and the MI358 Inhibitor
Authors: Chalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
A: Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta
B: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0874
Polymers90,0932
Non-polymers9942
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-9 kcal/mol
Surface area29840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.759, 101.155, 188.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta / PtdIns 4-kinase beta / NPIK / PI4K92 / PI4KB


Mass: 65264.766 Da / Num. of mol.: 1 / Fragment: UNP Residues 128-422, 523-799
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KB, PIK4CB / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase
#2: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 24827.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#3: Chemical ChemComp-5W6 / ~{N}-[2-[[6-chloranyl-3-[3-[4-(hydroxymethyl)piperidin-1-yl]sulfonyl-4-methoxy-phenyl]-2-methyl-imidazo[1,2-b]pyridazin-8-yl]amino]ethyl]ethanamide


Mass: 551.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H31ClN6O5S
#4: 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium chloride, 0.1M Tris PH=7, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.78→48.85 Å / Num. obs: 9508 / % possible obs: 96.34 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.211 / Net I/σ(I): 8.33 / Num. measured all: 51343
Reflection shellResolution: 3.78→3.92 Å / Mean I/σ(I) obs: 1.45 / % possible all: 91.53

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D0L

4d0l


Resolution: 3.789→48.849 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3016 471 4.99 %
Rwork0.248 --
obs0.2507 9439 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.789→48.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 65 0 5027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035125
X-RAY DIFFRACTIONf_angle_d0.896944
X-RAY DIFFRACTIONf_dihedral_angle_d15.61876
X-RAY DIFFRACTIONf_chiral_restr0.03797
X-RAY DIFFRACTIONf_plane_restr0.008868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7894-4.33750.30491510.30482891X-RAY DIFFRACTION95
4.3375-5.46360.31851570.26042972X-RAY DIFFRACTION97
5.4636-48.85340.2911630.22143105X-RAY DIFFRACTION96

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