[English] 日本語
Yorodumi
- PDB-8q6h: HUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q6h
TitleHUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOUND 11)
ComponentsPhosphatidylinositol 4-kinase beta
KeywordsTRANSFERASE / LIPID KINASE / TRANSFERASE-SIGNALING PROTEIN COMPLEX / COVALENT INHIBITOR.
Function / homology
Function and homology information


1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / lysosome organization / inner ear development / phosphatidylinositol phosphate biosynthetic process / receptor-mediated endocytosis ...1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / lysosome organization / inner ear development / phosphatidylinositol phosphate biosynthetic process / receptor-mediated endocytosis / 14-3-3 protein binding / kinase activity / mitochondrial outer membrane / endosome / phosphorylation / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / PI4KB/PIK1, accessory (PIK) domain / 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 ...: / PI4KB/PIK1, accessory (PIK) domain / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-KI7 / Phosphatidylinositol 4-kinase beta / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsSomers, D.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Chem Biol / Year: 2023
Title: Covalent targeting of non-cysteine residues in PI4KIII beta.
Authors: Cosgrove, B. / Grant, E.K. / Bertrand, S. / Down, K.D. / Somers, D.O. / P Evans, J. / Tomkinson, N.C.O. / Barker, M.D.
History
DepositionAug 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 4-kinase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0454
Polymers48,4041
Non-polymers6413
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-3 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.839, 67.845, 107.033
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 / PI4K-beta / PI4Kbeta / PtdIns 4-kinase beta / NPIK / PI4K92 / PI4KIII


Mass: 48403.625 Da / Num. of mol.: 1 / Mutation: R409Q,R412Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KB, PIK4CB, PI4KB / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: Q9UBF8, UniProt: A0A0B4J1S8, 1-phosphatidylinositol 4-kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-KI7 / 3-(3-fluorosulfonyloxy-4-methoxy-phenyl)-7-[(4-fluorosulfonyloxyphenyl)methylamino]-2,5-dimethyl-pyrazolo[1,5-a]pyrimidine


Mass: 554.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20F2N4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium Formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→57.303 Å / Num. obs: 20831 / % possible obs: 93.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.057 / Rrim(I) all: 0.146 / Net I/σ(I): 10
Reflection shellResolution: 1.94→2.088 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.464 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1042 / CC1/2: 0.516 / Rpim(I) all: 0.631 / Rrim(I) all: 1.598 / % possible all: 64

-
Processing

Software
NameVersionClassification
autoPROCv1.1.7data processing
XDSVERSION Jan 10, 2022data reduction
Aimlessv0.7.9data scaling
STARANISOv2.3.92data scaling
REFMAC5.8.0405phasing
REFMAC5.8.0405refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.94→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.022 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23679 1016 4.9 %RANDOM
Rwork0.16952 ---
obs0.17272 19774 64.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 40 249 3388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123244
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163117
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.6484399
X-RAY DIFFRACTIONr_angle_other_deg0.381.5777174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.642521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31910587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2567.3051559
X-RAY DIFFRACTIONr_mcbond_other5.2557.3051560
X-RAY DIFFRACTIONr_mcangle_it7.36914.0021951
X-RAY DIFFRACTIONr_mcangle_other7.36714.0021952
X-RAY DIFFRACTIONr_scbond_it6.7318.5791685
X-RAY DIFFRACTIONr_scbond_other6.7298.581686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.60216.1752449
X-RAY DIFFRACTIONr_long_range_B_refined11.28443.823753
X-RAY DIFFRACTIONr_long_range_B_other11.30242.343711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.162 7 -
Rwork0.272 154 -
obs--6.93 %

+
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