PDB-7em5: Crystal structure of the PI5P4Kbeta F205L-XTP complex

ID or keywords:

Entry

Database: PDB / ID: 7em5

Title

Crystal structure of the PI5P4Kbeta F205L-XTP complex

Components

Phosphatidylinositol 5-phosphate 4-kinase type-2 beta

Keywords

TRANSFERASE /

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Senda, M. / Senda, T.

Funding support

Japan, 1items

Citation

Journal: 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. / ...

History

Deposition	Apr 13, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 30, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 6, 2022	Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2	May 25, 2022	Group: 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 1.3	Jun 15, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7em5.cif.gz	261.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7em5.ent.gz	208.9 KB	Display	PDB format
PDBx/mmJSON format	7em5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/em/7em5 ftp://data.pdbj.org/pub/pdb/validation_reports/em/7em5	HTTPS FTP

-
Related structure data

Related structure data	6k4gSC 6k4hC 7em1C 7em2C 7em3C 7em4C 7em6C 7em7C 7em8C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (6) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #148 - Apr 2012 Ras Protein similarity (1)

Deposited unit

A: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta

B: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta

hetero molecules

91.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	109.561, 186.153, 105.655
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#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: 44894.887 Da / Num. of mol.: 2 / Mutation: F205L 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-CZC / [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate / xanthosine diphosphate Mass: 444.185 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₁₀H₁₄N₄O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CZF / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate / xanthosine triphosphate / Xanthosine triphosphate Mass: 524.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₄O₁₅P₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 9%(w/v) PEG4000, 0.1 M sodium citrate pH 6.0, 0.1 M magnesium acetate, 0.1 M lithium acetate

-
Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2018
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.8→48.63 Å / Num. obs: 26919 / % possible obs: 99.7 % / Redundancy: 8.9 % / R_merge(I) obs: 0.061 / Net I/σ(I): 25.48
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 8.5 % / R_merge(I) obs: 0.996 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 3787 / % possible all: 98.4

-
Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
XSCALE		data scaling
Coot		model building
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6K4G

6k4g

Resolution: 2.8→47.211 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.03

	R_factor	Num. reflection	% reflection
R_free	0.2607	1345	5 %
R_work	0.2168	-	-
obs	0.219	26898	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.8→47.211 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4661	0	88	2	4751

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4894
X-RAY DIFFRACTION	f_angle_d	1.106	6691
X-RAY DIFFRACTION	f_dihedral_angle_d	8.012	3507
X-RAY DIFFRACTION	f_chiral_restr	0.055	776
X-RAY DIFFRACTION	f_plane_restr	0.006	851

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.8-2.9001	0.3351	130	0.3034	2469	X-RAY DIFFRACTION	98
2.9001-3.0162	0.35	133	0.2984	2535	X-RAY DIFFRACTION	100
3.0162-3.1534	0.3501	133	0.2687	2529	X-RAY DIFFRACTION	100
3.1534-3.3196	0.3351	133	0.2456	2530	X-RAY DIFFRACTION	100
3.3196-3.5276	0.3308	134	0.2478	2545	X-RAY DIFFRACTION	100
3.5276-3.7998	0.2244	135	0.2147	2552	X-RAY DIFFRACTION	100
3.7998-4.182	0.2479	134	0.1941	2547	X-RAY DIFFRACTION	100
4.182-4.7866	0.2273	135	0.1745	2570	X-RAY DIFFRACTION	100
4.7866-6.0287	0.2386	137	0.2027	2603	X-RAY DIFFRACTION	100
6.0287-47.211	0.25	141	0.2239	2673	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.0173	2.4226	0.6749	3.5725	0.7848	3.8595	-0.2027	0.2847	-0.1751	-0.1226	0.3354	0.0747	0.149	0.4783	-0.1161	0.4609	0.0766	0.0861	0.5635	-0.0121	0.4705	43.0424	38.6787	-12.4141
2	4.466	1.1127	-0.2183	1.7313	1.7707	4.1643	-0.0061	-0.4897	0.3701	0.1617	0.012	0.3792	-0.1419	0.002	0.0995	0.5624	0.0695	0.1065	0.5035	0.0095	0.515	40.6091	47.6251	-2.5825
3	2.7859	-0.474	0.328	4.5282	1.3461	5.6276	-0.8686	0.3825	0.9366	-0.6203	0.9424	-1.3455	-0.235	1.9764	-0.2581	0.5157	-0.2881	0.1201	1.2022	-0.1786	0.6878	59.3941	50.1071	-11.0783
4	0.2157	-0.1092	0.811	3.709	1.7982	1.5498	-0.2481	0.0798	0.4229	0.0526	0.3119	0.2344	-0.4165	0.2349	-0.0003	0.4719	-0.1127	0.06	0.6721	0.006	0.589	47.2463	56.6286	-4.6882
5	4.0075	0.7638	-2.9598	5.6963	0.14	3.3737	0.1204	-0.2517	2.0331	-0.811	0.2748	0.5657	-0.8569	-0.4555	-0.4676	0.9187	0.0379	-0.0519	0.8181	-0.1939	1.3679	46.4269	73.1305	3.7335
6	3.0059	-0.4875	-0.5743	4.0339	2.4265	7.2265	-0.9791	0.9352	-0.5608	-0.7219	1.1602	0.0189	0.3139	0.7765	-0.1477	0.6451	-0.3537	0.1679	0.9732	-0.1832	0.8648	63.1306	60.739	0.0553
7	2.1721	-0.6009	0.3361	1.7452	0.4179	2.1203	-0.0132	-0.7419	0.5231	0.7537	0.012	-0.0388	0.236	-0.2045	-0.0908	0.8121	-0.0244	0.1313	0.931	-0.2404	0.7488	43.7337	60.7814	14.6254
8	2.8498	0.9189	-0.2738	3.4048	-1.631	1.5554	-0.3072	-0.263	0.5676	-0.953	0.8996	-0.5814	-0.4559	0.24	-0.8535	0.5741	-0.2066	0.2362	0.5163	-0.1392	0.725	53.4462	62.037	-2.3621
9	6.2581	-0.876	-5.39	4.5956	1.0444	4.9294	0.434	1.2305	1.2513	-1.1035	1.5534	-1.4293	-0.8994	0.8649	-2.1292	0.8566	-0.2399	0.1323	0.7635	-0.169	1.1361	61.1407	69.4239	-0.0732
10	2.5165	0.375	-0.7451	1.1839	0.3372	2.6986	0.057	0.4572	0.2253	-0.177	0.1226	-0.1493	-0.0297	0.139	-0.1426	0.5341	0.0509	0.0301	0.48	-0.0407	0.4552	35.1854	25.6126	-16.9801
11	3.2431	-0.4278	0.8543	2.5789	-1.3601	2.0135	-0.1341	0.0304	0.1581	0.4922	-0.0818	-0.1562	0.5641	0.1964	-0.022	0.756	0.0199	0.0403	0.4607	-0.0721	0.6771	36.5942	12.5645	-14.0726
12	3.0733	-0.5193	0.2977	3.5156	0.3379	3.3888	0.1522	0.3485	-0.3482	-0.1443	0.1423	0.3162	0.7427	-0.1087	-0.2146	0.6601	-0.0699	-0.093	0.3881	-0.1287	0.5176	27.1728	12.68	-20.4912
13	2.6583	0.1575	-0.1845	2.6397	0.2638	2.8028	-0.9806	0.2793	-0.6188	-1.3698	0.1176	-1.171	0.1896	1.2061	0.4919	1.4763	0.1563	0.1518	1.2931	-0.1374	0.9768	35.1469	-8.0103	-28.0623
14	2.7806	1.6271	-0.262	2.8444	-0.568	3.8772	-0.6261	1.9434	-3.6418	0.1687	-0.2536	-1.8336	0.8676	0.7471	0.0496	1.6244	0.0401	0.0097	0.85	-0.6183	1.9069	26.4882	-13.1883	-20.9693
15	5.2877	-1.0135	1.071	2.9319	1.2624	1.3879	-0.1949	0.2099	0.0842	-1.2324	0.6059	0.2711	0.8395	-0.0447	-0.0504	1.015	-0.297	-0.1583	0.7666	0.1063	1.2307	13.9059	2.2736	-20.7603
16	1.2656	-0.8354	0.0478	1.4236	1.2315	1.5644	0.4054	-0.2582	-0.6614	-1.336	0.0364	0.2474	2.0918	-0.2966	-0.1843	1.6545	0.0648	-0.0074	0.2534	-0.073	1.1098	28.7515	-5.4346	-11.2289
17	1.3008	-0.7769	0.6323	1.573	-0.1764	0.2954	0.9109	0.3391	-1.3459	-0.1631	-0.1749	-0.0269	1.5498	0.2589	-0.6184	1.6023	-0.2279	-0.3139	0.6694	-0.3057	0.9714	20.7913	-3.7477	-22.8707

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 33 through 110 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 111 through 153 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 154 through 174 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 175 through 227 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 228 through 253 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 254 through 279 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 280 through 360 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 361 through 399 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 400 through 416 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 33 through 109 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 110 through 153 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 154 through 212 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 213 through 236 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 237 through 258 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 259 through 274 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 275 through 360 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 361 through 416 )

-
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

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi