[English] 日本語
Yorodumi
- PDB-7em6: Crystal structure of the PI5P4Kbeta N203D-ITP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7em6
TitleCrystal structure of the PI5P4Kbeta N203D-ITP complex
ComponentsPhosphatidylinositol 5-phosphate 4-kinase type-2 beta
KeywordsTRANSFERASE / Lipid Kinase / Phosphoinositide signaling
Function / homology
Function and homology information


1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / negative regulation of insulin receptor signaling pathway / autophagosome / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phosphorylation / cell surface receptor signaling pathway / endoplasmic reticulum membrane / GTP binding / protein homodimerization activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol-4-phosphate 5-kinase / Phosphatidylinositol-4-phosphate 5-kinase, core / : / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CZU / INOSINE-5'-DIPHOSPHATE / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSenda, M. / Senda, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
CitationJournal: Structure / Year: 2022
Title: The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Authors: Takeuchi, K. / Ikeda, Y. / Senda, M. / Harada, A. / Okuwaki, K. / Fukuzawa, K. / Nakagawa, S. / Yu, H.Y. / Nagase, L. / Imai, M. / Sasaki, M. / Lo, Y.H. / Ito, D. / Osaka, N. / Fujii, Y. / ...Authors: Takeuchi, K. / Ikeda, Y. / Senda, M. / Harada, A. / Okuwaki, K. / Fukuzawa, K. / Nakagawa, S. / Yu, H.Y. / Nagase, L. / Imai, M. / Sasaki, M. / Lo, Y.H. / Ito, D. / Osaka, N. / Fujii, Y. / Sasaki, A.T. / Senda, T.
History
DepositionApr 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
B: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2245
Polymers89,8602
Non-polymers1,3653
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-22 kcal/mol
Surface area27580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.079, 186.438, 106.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Phosphatidylinositol 5-phosphate 4-kinase type-2 beta / 1-phosphatidylinositol 5-phosphate 4-kinase 2-beta / Diphosphoinositide kinase 2-beta / ...1-phosphatidylinositol 5-phosphate 4-kinase 2-beta / Diphosphoinositide kinase 2-beta / Phosphatidylinositol 5-phosphate 4-kinase type II beta / PI(5)P 4-kinase type II beta / PIP4KII-beta / PtdIns(5)P-4-kinase isoform 2-beta


Mass: 44929.891 Da / Num. of mol.: 2 / Mutation: N203D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4K2B, PIP5K2B / Production host: Escherichia coli (E. coli)
References: UniProt: P78356, 1-phosphatidylinositol-5-phosphate 4-kinase
#2: Chemical ChemComp-IDP / INOSINE-5'-DIPHOSPHATE


Mass: 428.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CZU / [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate / Inosine-5'-triphosphate


Mass: 508.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N4O14P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 9%(w/v) PEG4000, 0.1M sodium citrate pH 6.0, 0.1M magnesium acetate, 0.1M lithium acetate

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2018
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.95→48.3 Å / Num. obs: 23179 / % possible obs: 99.9 % / Redundancy: 9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.52
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 2.71 / Num. unique obs: 3308 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K4G

6k4g


Resolution: 2.95→35.687 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 1160 5 %
Rwork0.2139 --
obs0.2165 22934 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→35.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 85 0 4718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094822
X-RAY DIFFRACTIONf_angle_d1.1066578
X-RAY DIFFRACTIONf_dihedral_angle_d7.9652906
X-RAY DIFFRACTIONf_chiral_restr0.057763
X-RAY DIFFRACTIONf_plane_restr0.006839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.08420.37461440.31652722X-RAY DIFFRACTION100
3.0842-3.24670.41361420.29622702X-RAY DIFFRACTION100
3.2467-3.450.34521430.26322720X-RAY DIFFRACTION100
3.45-3.71610.27911440.22712731X-RAY DIFFRACTION100
3.7161-4.08960.23471440.20312735X-RAY DIFFRACTION100
4.0896-4.68020.24191450.17942758X-RAY DIFFRACTION100
4.6802-5.89230.2311460.19452773X-RAY DIFFRACTION100
5.8923-35.6870.26551520.21092878X-RAY DIFFRACTION99
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)
14.28363.46051.97064.92541.82956.3169-0.03530.5678-0.1393-0.09720.2658-0.0430.39560.4312-0.14520.46830.06950.09860.47050.02720.483343.026539.189-12.6242
26.48620.9723-0.71633.59124.6517.095-0.3635-0.34520.43420.38840.27390.3827-0.2661-0.19320.06720.6662-0.00870.0540.48170.00770.588540.668447.8797-2.9831
32.438-0.83460.61625.93724.08665.9817-0.11550.16520.6628-0.01410.6309-0.2958-0.24841.0234-0.42220.4232-0.21720.04680.7801-0.01840.709750.242853.3379-6.5168
42.20182.1173-1.4552.7099-1.15825.76180.22090.32061.98880.28260.24010.9316-1.56870.3455-0.42851.0633-0.06280.0180.89960.08591.316646.934974.12941.3451
58.19841.02760.58465.74021.68834.0698-1.19220.3985-0.5046-0.09490.32530.01090.32720.27750.53610.6544-0.02560.06690.782-0.14560.616452.885162.39375.7168
65.71322.2063-0.70754.08791.94815.71280.035-0.01740.81240.24750.7359-0.6604-0.07740.3751-0.76010.5794-0.06680.06560.7103-0.26371.02953.764463.27845.2115
75.71223.1085-0.24672.7810.35863.5461-0.36440.4020.062-0.20510.4041-0.35050.24120.0035-0.05270.64940.06320.0430.4638-0.030.518235.01625.8593-17.0382
88.5111-0.10382.74724.7737-4.80116.394-0.01010.0568-0.5164-0.0998-0.50320.01861.33630.2740.52271.04830.06860.11580.5272-0.02430.724336.810412.9719-13.8299
94.601-0.5133-0.79964.9175-1.10715.398-0.10580.3681-0.329-0.45510.43670.4921.1171-0.2376-0.33540.7857-0.1816-0.06640.4607-0.14370.597127.30612.8502-20.6092
102.7488-0.01021.71115.1351-1.25593.54430.34750.8391-1.1003-0.9565-0.13380.27512.67650.1114-0.31721.7887-0.0306-0.04850.6775-0.20521.153425.1974-5.2866-19.8082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 153 )
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 217 )
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 253 )
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 300 )
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 416 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 109 )
8X-RAY DIFFRACTION8chain 'B' and (resid 110 through 153 )
9X-RAY DIFFRACTION9chain 'B' and (resid 154 through 212 )
10X-RAY DIFFRACTION10chain 'B' and (resid 213 through 416 )

+
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