[English] 日本語
Yorodumi
- PDB-5fbw: PI4KB in complex with Rab11 and the MI369 Inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fbw
TitlePI4KB in complex with Rab11 and the MI369 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


1-phosphatidylinositol 4-kinase activity / 1-phosphatidylinositol 4-kinase / regulation of multivesicular body size / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / rough endoplasmic reticulum membrane / exosomal secretion / melanosome transport ...1-phosphatidylinositol 4-kinase activity / 1-phosphatidylinositol 4-kinase / regulation of multivesicular body size / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / rough endoplasmic reticulum membrane / exosomal secretion / melanosome transport / Synthesis of PIPs at the Golgi membrane / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / amyloid-beta clearance by transcytosis / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / multivesicular body assembly / phosphatidylinositol biosynthetic process / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / mitotic metaphase plate congression / lysosome organization / phosphatidylinositol kinase activity / syntaxin binding / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / positive regulation of axon extension / 14-3-3 protein binding / mitotic spindle assembly / centriolar satellite / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / Vasopressin regulates renal water homeostasis via Aquaporins / phagocytic vesicle / receptor-mediated endocytosis / G protein activity / transport vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / small monomeric GTPase / multivesicular body / vesicle-mediated transport / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / regulation of cytokinesis / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / spindle pole / recycling endosome membrane / neuron projection development / microtubule binding / cytoplasmic vesicle / mitochondrial outer membrane / vesicle / endosome / axon / centrosome / GTPase activity / Golgi membrane / glutamatergic synapse / intracellular membrane-bounded organelle / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / membrane / ATP binding / cytosol / cytoplasm
Similarity search - Function
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-kinases catalytic domain profile. ...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-kinases catalytic domain profile. / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / 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
Ras-related protein Rab-11A / Chem-5W8 / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.487 Å
AuthorsChalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E.
CitationJournal: To Be Published
Title: PI4KB in complex with Rab11 and the MI369 Inhibitor
Authors: Chalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E.
History
DepositionDec 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)91,1424
Polymers90,0782
Non-polymers1,0642
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-16 kcal/mol
Surface area30240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.066, 104.091, 187.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 65264.766 Da / Num. of mol.: 1
Fragment: UNP Residues 128-422, 523-729,UNP Residues 128-422, 523-729
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: 24813.000 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-5W8 / ~{N}-[2-[[6-chloranyl-3-[4-methoxy-3-[[(2~{R})-1-oxidanylbutan-2-yl]sulfamoyl]phenyl]-2-methyl-imidazo[1,2-b]pyridazin-8-yl]amino]ethyl]ethanamide


Mass: 525.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29ClN6O5S
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 0.1M MES pH=6.5, 20% (w/v) PEG 8000

-
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: 3.48→47.47 Å / Num. obs: 12696 / % possible obs: 98.32 % / Redundancy: 4.27 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 6.77 / Num. measured all: 54212
Reflection shellResolution: 3.48→3.61 Å / Mean I/σ(I) obs: 0.87

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D0L
Resolution: 3.487→47.469 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 629 4.98 %Random selection
Rwork0.2462 ---
obs0.248 12626 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.487→47.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 67 0 5023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055123
X-RAY DIFFRACTIONf_angle_d1.1476946
X-RAY DIFFRACTIONf_dihedral_angle_d16.1681854
X-RAY DIFFRACTIONf_chiral_restr0.048794
X-RAY DIFFRACTIONf_plane_restr0.007867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4866-3.83730.3781510.36812882X-RAY DIFFRACTION96
3.8373-4.39230.34011560.26542955X-RAY DIFFRACTION99
4.3923-5.53250.28011570.2493003X-RAY DIFFRACTION98
5.5325-47.4730.24411650.21063157X-RAY DIFFRACTION99

+
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