[English] 日本語
Yorodumi
- PDB-8ppc: Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ppc
TitleHuman inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with L-chiro-inositol 2,3,5-trisphosphate/ATP/Mn
ComponentsInositol-trisphosphate 3-kinase A
KeywordsTRANSFERASE / Inositol polyphosphate / InsP / inositol kinase / IP3K / calcium / InsP3 / IP3 / IPK / IP3 3-K
Function / homology
Function and homology information


inositol-trisphosphate 3-kinase / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / modification of postsynaptic actin cytoskeleton / inositol phosphate biosynthetic process / postsynaptic actin cytoskeleton / inositol metabolic process / positive regulation of dendritic spine morphogenesis / dendritic spine maintenance / calmodulin-dependent protein kinase activity ...inositol-trisphosphate 3-kinase / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / modification of postsynaptic actin cytoskeleton / inositol phosphate biosynthetic process / postsynaptic actin cytoskeleton / inositol metabolic process / positive regulation of dendritic spine morphogenesis / dendritic spine maintenance / calmodulin-dependent protein kinase activity / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol phosphate biosynthetic process / cellular response to calcium ion / regulation of synaptic plasticity / small GTPase binding / response to calcium ion / actin cytoskeleton organization / dendritic spine / cytoskeleton / calmodulin binding / phosphorylation / glutamatergic synapse / signal transduction / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase
Similarity search - Domain/homology
: / ADENOSINE-5'-TRIPHOSPHATE / : / Inositol-trisphosphate 3-kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.92 Å
AuthorsMarquez-Monino, M.A. / Gonzalez, B.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117400GB-100 Spain
Spanish Ministry of Economy and CompetitivenessBFU2017-89913-P Spain
CitationJournal: Nat Commun / Year: 2024
Title: Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity.
Authors: Marquez-Monino, M.A. / Ortega-Garcia, R. / Whitfield, H. / Riley, A.M. / Infantes, L. / Garrett, S.W. / Shipton, M.L. / Brearley, C.A. / Potter, B.V.L. / Gonzalez, B.
History
DepositionJul 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inositol-trisphosphate 3-kinase A
B: Inositol-trisphosphate 3-kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,29514
Polymers63,7552
Non-polymers2,54112
Water4,918273
1
A: Inositol-trisphosphate 3-kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1487
Polymers31,8771
Non-polymers1,2706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol-trisphosphate 3-kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1487
Polymers31,8771
Non-polymers1,2706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.915, 97.904, 191.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-506-

SO4

21B-731-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Inositol-trisphosphate 3-kinase A / Inositol 1 / 4 / 5-trisphosphate 3-kinase A / IP3 3-kinase A / IP3K A / InsP 3-kinase A


Mass: 31877.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Catalytic domain / Source: (gene. exp.) Homo sapiens (human) / Gene: ITPKA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star
References: UniProt: P23677, inositol-trisphosphate 3-kinase

-
Non-polymers , 5 types, 285 molecules

#2: Chemical ChemComp-2KM / L-chiro-inositol 2,3,5-trisphosphate / [(1R,2R,3R,4R,5S,6R)-2,3,5-tris(oxidanyl)-4,6-diphosphonooxy-cyclohexyl] dihydrogen phosphate


Mass: 420.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O15P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.29 % / Description: Cube / Trapezoidal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.80 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 9 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. ...Details: 0.80 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 9 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979264 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2021 / Details: KB mirrors, rectangular beam shape
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979264 Å / Relative weight: 1
ReflectionResolution: 1.92→49.66 Å / Num. obs: 51230 / % possible obs: 98.4 % / Redundancy: 10 % / Biso Wilson estimate: 31.616 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.032 / Net I/σ(I): 13.3
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2906 / CC1/2: 0.799 / Rpim(I) all: 0.299 / % possible all: 84.8

-
Processing

Software
NameVersionClassification
REFMACv5.8.0258refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.92→49.66 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.385 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21886 2659 5.2 %RANDOM
Rwork0.1932 ---
obs0.19451 48515 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.024 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---0.56 Å20 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.92→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4425 0 142 273 4840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134700
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174311
X-RAY DIFFRACTIONr_angle_refined_deg1.51.6586361
X-RAY DIFFRACTIONr_angle_other_deg1.3161.599973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.28320288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01115834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3361557
X-RAY DIFFRACTIONr_chiral_restr0.0680.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021072
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_it3.3394.1682225
X-RAY DIFFRACTIONr_mcbond_other3.3334.1662224
X-RAY DIFFRACTIONr_mcangle_it4.6946.2232783
X-RAY DIFFRACTIONr_mcangle_other4.6956.2252784
X-RAY DIFFRACTIONr_scbond_it4.1294.722475
X-RAY DIFFRACTIONr_scbond_other4.0294.6842451
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1156.8383543
X-RAY DIFFRACTIONr_long_range_B_refined7.99748.3235254
X-RAY DIFFRACTIONr_long_range_B_other7.9748.1725214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2089medium positional0.50.5
1264tight thermal2.870.5
2089medium thermal3.362
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 157 -
Rwork0.38 3058 -
obs--84.32 %

+
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://pdbjlvh1.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