[English] 日本語
Yorodumi
- PDB-6osp: Crystal Structure Analysis of PIP4K2A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6osp
TitleCrystal Structure Analysis of PIP4K2A
ComponentsPhosphatidylinositol 5-phosphate 4-kinase type-2 alpha
KeywordsTRANSFERASE / kinase / SIGNALING PROTEIN
Function / homology
Function and homology information


vesicle-mediated cholesterol transport / 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 / megakaryocyte development / PI5P Regulates TP53 Acetylation ...vesicle-mediated cholesterol transport / 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 / megakaryocyte development / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / photoreceptor outer segment / autophagosome / negative regulation of insulin receptor signaling pathway / photoreceptor inner segment / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / lysosome / phosphorylation / protein homodimerization activity / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / 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 Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / 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-N51 / Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Cell Chem Biol / Year: 2020
Title: Targeting the PI5P4K Lipid Kinase Family in Cancer Using Covalent Inhibitors.
Authors: Sivakumaren, S.C. / Shim, H. / Zhang, T. / Ferguson, F.M. / Lundquist, M.R. / Browne, C.M. / Seo, H.S. / Paddock, M.N. / Manz, T.D. / Jiang, B. / Hao, M.F. / Krishnan, P. / Wang, D.G. / ...Authors: Sivakumaren, S.C. / Shim, H. / Zhang, T. / Ferguson, F.M. / Lundquist, M.R. / Browne, C.M. / Seo, H.S. / Paddock, M.N. / Manz, T.D. / Jiang, B. / Hao, M.F. / Krishnan, P. / Wang, D.G. / Yang, T.J. / Kwiatkowski, N.P. / Ficarro, S.B. / Cunningham, J.M. / Marto, J.A. / Dhe-Paganon, S. / Cantley, L.C. / Gray, N.S.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 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
A: Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
B: Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7136
Polymers90,4662
Non-polymers1,2474
Water4,035224
1
A: Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8573
Polymers45,2331
Non-polymers6242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8573
Polymers45,2331
Non-polymers6242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-10 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.190, 98.680, 105.120
Angle α, β, γ (deg.)90.000, 93.660, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha / 1-phosphatidylinositol 5-phosphate 4-kinase 2-alpha / Diphosphoinositide kinase 2-alpha / PIP5KIII ...1-phosphatidylinositol 5-phosphate 4-kinase 2-alpha / Diphosphoinositide kinase 2-alpha / PIP5KIII / Phosphatidylinositol 5-phosphate 4-kinase type II alpha / PIP4KII-alpha / PtdIns(4)P-5-kinase B isoform / PtdIns(4)P-5-kinase C isoform / PtdIns(5)P-4-kinase isoform 2-alpha


Mass: 45233.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4K2A, PIP5K2, PIP5K2A / Production host: Escherichia coli (E. coli)
References: UniProt: P48426, 1-phosphatidylinositol-5-phosphate 4-kinase
#2: Chemical ChemComp-N51 / 4-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}-N-(3-{[6-(1H-indol-3-yl)pyrimidin-4-yl]amino}phenyl)benzamide


Mass: 531.608 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C31H29N7O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, 200mM Malic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.21→46.32 Å / Num. obs: 44869 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 38.865 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.079 / Net I/σ(I): 13.1 / Num. measured all: 168656
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.21-2.253.81.3828021930.6061.18199
5.99-46.333.640844423180.0130.02599.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
XDSdata reduction
xia2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YBX

2ybx


Resolution: 2.21→44.648 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 2331 5.2 %
Rwork0.1773 42504 -
obs0.1798 44835 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.45 Å2 / Biso mean: 55.1703 Å2 / Biso min: 27.55 Å2
Refinement stepCycle: final / Resolution: 2.21→44.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5093 0 108 224 5425
Biso mean--73.84 51.71 -
Num. residues----630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.25510.37051350.33172424255999
2.2551-2.30420.36411420.292478262099
2.3042-2.35770.37011300.25112500263099
2.3577-2.41670.25041430.23552461260499
2.4167-2.4820.29671270.2342517264499
2.482-2.55510.30731210.22124882609100
2.5551-2.63750.30321310.21972517264899
2.6375-2.73180.31411420.22122486262899
2.7318-2.84120.28131190.216725032622100
2.8412-2.97040.27961570.208324962653100
2.9704-3.1270.23491300.187325182648100
3.127-3.32290.2321310.189525082639100
3.3229-3.57930.24391190.178725292648100
3.5793-3.93930.21661720.151424822654100
3.9393-4.50890.17471530.134825202673100
4.5089-5.67890.16311530.130525042657100
5.6789-44.65730.17451260.15692573269999
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)
10.96770.8794-0.332.16420.17472.1702-0.2134-0.33570.22710.64140.02330.13040.2763-0.107-0.00310.63950.03850.01680.7156-0.0320.5789-45.6423-11.794154.8955
22.5742-1.4894-0.71521.3771-0.83813.22780.165-0.2393-0.51590.35360.1909-0.95730.34940.87190.18150.4542-0.0291-0.04260.575-0.10460.4109-36.4717-11.980850.6329
33.4283-0.5510.54730.88280.35565.9736-0.1069-0.22650.16090.10750.2014-0.3173-0.56530.3561-0.00610.48060.016-0.00450.5814-0.02340.4024-38.6882-6.259449.9233
40.6464-0.35740.43420.2538-0.3630.56160.2031-0.719-0.211.0642-0.39890.87590.9822-0.8493-0.00170.7574-0.11240.04040.86190.17620.7171-47.8307-19.610656.6472
50.6150.2201-0.07621.5595-0.16821.29210.2146-0.6088-0.11450.2028-0.14460.08790.0432-0.4551-0.00030.41230.04260.03310.4855-0.00060.4525-39.5306-9.69755.6966
60.80280.0801-0.89651.3652-0.65532.2926-0.0335-0.1685-0.1853-0.0288-0.0893-0.15260.17450.08270.00040.41720.00770.00280.4178-0.00730.422-29.2821-14.07675.1619
72.2516-0.0554-0.82822.259-1.87561.87830.14460.10870.42470.2595-0.09950.1043-0.2528-0.3530.00240.42610.0269-0.02220.4807-0.00170.4152-36.7027-2.2668-1.3817
82.12750.455-0.28081.6997-0.20683.1991-0.08850.3664-0.0826-0.1234-0.0119-0.12560.22830.0235-0.00070.3964-0.00440.01660.2992-0.01450.3964-27.5875-9.8283-9.1731
91.9211-0.1018-0.01792.6703-1.81163.6251-0.10970.3206-0.1351-0.2329-0.04050.19460.1503-0.2542-0.00270.3807-0.0118-0.00690.3325-0.07240.4007-33.924-6.4541-14.8127
101.7947-1.0209-0.27161.5461-0.72641.4009-0.19090.50540.0403-0.26440.01160.8959-0.1527-0.85770.00490.66740.0122-0.07170.6774-0.02570.5545-38.07650.8935-30.3098
112.9799-0.0540.84652.024-0.65863.319-0.25020.10680.1786-0.2507-0.0041-0.2732-0.36990.0868-0.00670.43060.0063-0.01120.3897-0.04510.3767-25.62171.1412-22.5748
124.3919-0.8930.12631.6901-1.79065.5811-0.1410.0877-0.14390.0725-0.19740.1445-0.2867-0.2017-0.02080.3945-0.0031-0.02210.3844-0.010.4376-31.77682.134-19.9177
130.96660.62440.46650.46410.05321.21850.37771.29270.2019-1.1397-0.5053-0.85870.46390.5636-0.01030.63320.00640.03310.70830.02290.5475-21.8594-5.3811-31.0681
140.92920.0155-0.39281.1195-0.16281.15750.31110.41480.3451-0.3112-0.2975-0.3613-0.00370.5055-0.00080.4089-0.03070.00170.47260.07180.4754-30.1156-11.944420.5565
150.84840.3595-1.03721.0938-0.1423.00520.02170.14980.0605-0.0124-0.10450.11330.2338-0.3364-0.00010.4024-0.01860.00170.40390.03490.437-40.2785-16.428119.5826
163.0161.0146-0.74981.92410.08083.5022-0.0822-0.2510.01050.1085-0.0788-0.10140.04520.04360.00030.39580.0028-0.02020.38570.0190.4021-39.1838-13.651632.9259
172.38950.8134-0.25481.5701-0.12262.9045-0.0221-0.46830.01560.109-0.11140.00760.0517-0.0173-0.00050.3711-0.0029-0.01230.41680.01260.398-37.4831-14.148735.6796
180.2711-0.30120.1070.65720.49951.22480.0759-0.5146-0.44540.0722-0.1753-1.1420.67010.9019-0.0040.76350.1409-0.06680.95140.07910.9143-29.603-19.286854.3366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 235 through 269 )B235 - 269
2X-RAY DIFFRACTION2chain 'B' and (resid 270 through 288 )B270 - 288
3X-RAY DIFFRACTION3chain 'B' and (resid 289 through 389 )B289 - 389
4X-RAY DIFFRACTION4chain 'B' and (resid 390 through 405 )B390 - 405
5X-RAY DIFFRACTION5chain 'A' and (resid 28 through 54 )A28 - 54
6X-RAY DIFFRACTION6chain 'A' and (resid 55 through 104 )A55 - 104
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 133 )A105 - 133
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 168 )A134 - 168
9X-RAY DIFFRACTION9chain 'A' and (resid 169 through 224 )A169 - 224
10X-RAY DIFFRACTION10chain 'A' and (resid 225 through 248 )A225 - 248
11X-RAY DIFFRACTION11chain 'A' and (resid 249 through 288 )A249 - 288
12X-RAY DIFFRACTION12chain 'A' and (resid 289 through 389 )A289 - 389
13X-RAY DIFFRACTION13chain 'A' and (resid 390 through 405 )A390 - 405
14X-RAY DIFFRACTION14chain 'B' and (resid 28 through 54 )B28 - 54
15X-RAY DIFFRACTION15chain 'B' and (resid 55 through 104 )B55 - 104
16X-RAY DIFFRACTION16chain 'B' and (resid 105 through 168 )B105 - 168
17X-RAY DIFFRACTION17chain 'B' and (resid 169 through 207 )B169 - 207
18X-RAY DIFFRACTION18chain 'B' and (resid 208 through 234 )B208 - 234

+
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