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- PDB-7em3: Crystal structure of the PI5P4Kbeta-2a-ATP complex -

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Basic information

Entry
Database: PDB / ID: 7em3
TitleCrystal structure of the PI5P4Kbeta-2a-ATP 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-CX0 / Chem-CXC / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)90,8224
Polymers89,8582
Non-polymers9642
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-12 kcal/mol
Surface area28310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.818, 185.947, 106.238
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALILEILE(chain 'A' and ((resid 33 and (name N or name...AA33 - 12710 - 104
12ARGARGLEULEU(chain 'A' and ((resid 33 and (name N or name...AA138 - 217115 - 194
13VALVALGLUGLU(chain 'A' and ((resid 33 and (name N or name...AA222 - 292199 - 269
14GLYGLYTHRTHR(chain 'A' and ((resid 33 and (name N or name...AA338 - 372315 - 349
15PROPROILEILE(chain 'A' and ((resid 33 and (name N or name...AA400 - 414377 - 391
26VALVALILEILE(chain 'B' and (resid 33 through 64 or (resid 65...BB33 - 12710 - 104
27ARGARGLEULEU(chain 'B' and (resid 33 through 64 or (resid 65...BB138 - 217115 - 194
28VALVALGLUGLU(chain 'B' and (resid 33 through 64 or (resid 65...BB222 - 292199 - 269
29GLYGLYTHRTHR(chain 'B' and (resid 33 through 64 or (resid 65...BB338 - 372315 - 349
210PROPROILEILE(chain 'B' and (resid 33 through 64 or (resid 65...BB400 - 414377 - 391

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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 / PIP4KII-beta / PtdIns(5)P-4-kinase isoform 2-beta


Mass: 44928.902 Da / Num. of mol.: 2
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-CX0 / [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate


Mass: 442.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CXC / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 17, 2018
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→48.78 Å / Num. obs: 20095 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 103.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 24.55
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.896 / Num. unique obs: 2925 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K4H

6k4h


Resolution: 3.1→46.12 Å / SU ML: 0.3648 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1449
RfactorNum. reflection% reflection
Rfree0.2559 1004 5 %
Rwork0.2126 --
obs0.2148 20085 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 109.76 Å2
Refinement stepCycle: LAST / Resolution: 3.1→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 60 0 4634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01014741
X-RAY DIFFRACTIONf_angle_d1.22716482
X-RAY DIFFRACTIONf_chiral_restr0.0731752
X-RAY DIFFRACTIONf_plane_restr0.0079837
X-RAY DIFFRACTIONf_dihedral_angle_d6.88692830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.260.31131400.28242670X-RAY DIFFRACTION99.93
3.26-3.470.29661420.26492696X-RAY DIFFRACTION99.96
3.47-3.740.29091420.22272698X-RAY DIFFRACTION100
3.74-4.110.25621430.19812711X-RAY DIFFRACTION100
4.11-4.710.2251430.18712713X-RAY DIFFRACTION99.96
4.71-5.930.25511440.20062749X-RAY DIFFRACTION99.93
5.93-46.120.24831500.21712844X-RAY DIFFRACTION99.53
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)
14.750490616841.940779409542.339484669714.307335364461.117034554294.35134303440.01747527965640.2455687861960.0213116517584-0.2543762572820.198262397230.09505780849960.1830406913780.475169502976-0.1847323038370.523766377337-0.01935423948070.1229070282390.5701434288020.09925753411480.4746924699143.050792672338.6264571494-12.2256738057
29.597333529632.04701544156-1.670678459772.591363872023.641770155557.520322057090.00574050655141-1.1886486920.127632310403-0.0475698187126-0.01386927684230.4577400075360.341502910756-0.126329344070.05937373668130.6958384671840.05870737788770.1083225671320.630508873753-0.05728058425650.65883954578840.673364968247.3159189595-2.73963592032
34.84295115107-0.582111466338-1.71640563476.221423759884.217614220193.91908524475-0.473317872385-0.1578488778270.70656993953-0.05867505352560.913913789837-0.325887689308-0.3817595112251.028448065-0.4240895847130.446845123422-0.166482889590.05338161935450.716741455641-0.02527141035580.62871343704750.740729764651.1297929046-7.28026364454
43.99665233266-1.834034977390.7783957423825.58510678910.6735843945810.0146657897-0.03696709377640.52761501691.60295476627-0.2760241259340.4493374699980.137020782288-1.8810345691-0.494387944087-0.4673819384961.046605735870.005682080018990.04585074086181.180751195040.1974070135671.6059453001646.959107921772.72297830622.18287887964
57.697269800831.480491262510.7268582718373.825963133231.529735526162.31963440601-1.116600620570.1811249431120.175339771464-0.005777963498790.3713100947060.1168535327580.178379459908-0.3097961429990.7405401969530.867727261046-0.1165110655490.07586654003660.803717452145-0.2443017512110.99667323776252.121594555261.77011632736.91109312831
67.050193840.989143202515-2.527507677864.590811156081.63556223544.27830708560.000343666445143-0.588819227221.75301208046-0.09796621001750.721860723277-0.01094345477160.02610862232461.43444339819-0.7212787625490.6430538016640.0175445343605-0.009412986315130.841557163741-0.3019864860811.0972869565954.482350964362.87676560445.77064351894
74.022631462680.354525999195-0.6487472401772.921678158670.6556939464382.574187713490.1477336312780.1491022191660.289077840959-0.03509621440940.145077882673-0.177972492237-0.2851397849680.160470564841-0.2288012419610.767802244768-0.007908443050720.04392395381240.738741518421-0.0510850634540.59016383521534.936318408225.6164587169-17.0412243684
84.119687680220.2355479129172.736139485983.4098707938-2.887198400564.332873510140.5106188792430.1230772847650.16884794035-0.0523652220135-0.0234788484537-0.3607811203630.7477276638520.296976930504-0.4412287448551.144201421580.09280208090810.04347760383370.574012147027-0.02926780120590.90367993512436.646319042612.6280841645-14.0853796512
96.48083006498-0.5119770681720.4733602360945.770175360641.027842353576.973293518140.03633101381280.895162745297-0.870342865831-0.3346786971090.27691993390.4432545325180.7591662235740.545533351126-0.1400045996990.780990289707-0.0307702808104-0.1111409790890.511230454036-0.2459354383780.72388184288727.252604890712.5023591851-20.5435150906
104.350412163190.9407557682350.5430640552031.71728142455-2.110868551394.04399771223-1.082270377341.14065940174-2.01479918912-1.342481618120.3255898997-0.4775401701040.965755550856-0.2780416734850.5725500878381.91876007013-0.09235696131220.07447831275621.20201989245-0.4765506547841.3481246604530.5493919046-10.9228706559-24.9201886809
115.08454610533-4.194552373662.435818449635.5380971354-4.27793006324.051774497940.9356805992880.337073677436-1.34288499585-1.80986442457-0.2460596675170.9282484084373.91998483532-0.595879695947-0.9454439797972.23252803847-0.0578761253846-0.3682033744510.6716210611740.01879328666541.3208830675921.2403048286-2.07601453599-18.6921659708
122.239681410180.092953949697-1.220533169154.930981748871.843704145471.886267189190.847631061315-0.42245784581-0.444357393461-1.80789626128-0.2389571501311.453174156041.67554772693-0.239264239735-0.5188670198621.63545064004-0.164264803936-0.1854234301660.520332046254-0.05190893079021.244044837129.1420908407-6.17439200812-5.40550034047
131.440974845440.6827113657410.6885264704110.3884970299120.3312768693460.2772152343270.647547817608-0.114115951323-0.390355764944-1.06728936141-0.2489529020741.134449433332.18213713668-0.47969578975-0.5183530894941.92408652797-0.274644830174-0.5424509170590.848833376367-0.1778774751651.2809828211820.6845608467-2.98225863763-23.6929542271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 153 )
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 212 )
4X-RAY DIFFRACTION4chain 'A' and (resid 213 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 254 )
11X-RAY DIFFRACTION11chain 'B' and (resid 255 through 292 )
12X-RAY DIFFRACTION12chain 'B' and (resid 293 through 360 )
13X-RAY DIFFRACTION13chain 'B' and (resid 361 through 415 )

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