[English] 日本語
Yorodumi
- PDB-5c4g: Crystal structure of an engineered construct of phosphatidylinosi... -

+
Open data


ID or keywords:

Loading...

-
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 protein localization to centrosome / synaptic vesicle endosomal processing / : / 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 protein localization to centrosome / synaptic vesicle endosomal processing / : / 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 / establishment of vesicle localization / rough endoplasmic reticulum membrane / regulation of cilium assembly / amyloid-beta clearance by transcytosis / regulation of protein transport / presynaptic endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / exosomal secretion / vesicle-mediated transport in synapse / plasma membrane to endosome transport / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / regulation of vesicle-mediated transport / protein transmembrane transport / myosin V binding / RAB geranylgeranylation / astral microtubule organization / multivesicular body assembly / phosphatidylinositol biosynthetic process / protein localization to cilium / melanosome transport / 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 / mitotic metaphase chromosome alignment / lysosome organization / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / inner ear development / exocytosis / 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 / multivesicular body / 14-3-3 protein binding / Anchoring of the basal body to the plasma membrane / receptor-mediated endocytosis / 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 / centriole / trans-Golgi network / regulation of long-term neuronal synaptic plasticity / recycling endosome / Schaffer collateral - CA1 synapse / recycling endosome membrane / spindle pole / neuron projection development / 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 ...: / : / 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
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

-
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)86,3887
Polymers85,3762
Non-polymers1,0125
Water00
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

-
Components

-
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

-
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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 )

+
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