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- PDB-7em7: Crystal structure of the PI5P4Kbeta N203D-XTP complex -

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Basic information

Entry
Database: PDB / ID: 7em7
TitleCrystal structure of the PI5P4Kbeta N203D-XTP 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 / phosphatidylinositol phosphate biosynthetic process / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane ...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 / phosphatidylinositol phosphate biosynthetic process / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / negative regulation of insulin receptor signaling pathway / autophagosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell surface receptor signaling pathway / regulation of autophagy / 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-CZC / Chem-CZF / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 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 1.1Apr 6, 2022Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2May 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 1.3Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)90,8284
Polymers89,8602
Non-polymers9682
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-13 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.213, 185.857, 106.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 33 through 34 and (name N...
d_2ens_1(chain "B" and ((resid 33 through 34 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALGLUA2 - 203
d_12ens_1GLNGLNA205
d_13ens_1GLYLYSA210 - 215
d_14ens_1PHEGLNA217 - 250
d_15ens_1GLYPROA259 - 279
d_16ens_1GLUTHRA282 - 293
d_17ens_1GLUILEA297 - 310
d_21ens_1VALLYSD1 - 177
d_22ens_1VALGLUD181 - 205
d_23ens_1GLNGLND207
d_24ens_1GLYLYSD212 - 217
d_25ens_1PHETHRD219 - 285
d_26ens_1GLUILED288 - 301

NCS oper: (Code: givenMatrix: (-0.999567279031, 0.00608285041956, -0.0287793957666), (0.0119951680711, -0.8090492602, -0.587618422544), (-0.0268583438221, -0.58770936142, 0.808626202807)Vector: 77. ...NCS oper: (Code: given
Matrix: (-0.999567279031, 0.00608285041956, -0.0287793957666), (0.0119951680711, -0.8090492602, -0.587618422544), (-0.0268583438221, -0.58770936142, 0.808626202807)
Vector: 77.6385070992, 49.3723939485, 17.1982943171)

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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 / 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
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.: 1 / Source method: obtained synthetically / 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


Mass: 524.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N4O15P3
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: 59.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→48.64 Å / Num. obs: 14659 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 118.61 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.08
Reflection shellResolution: 3.45→3.64 Å / Rmerge(I) obs: 0.891 / Num. unique obs: 2134

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C55

7c55
PDB Unreleased entry


Resolution: 3.45→48.64 Å / SU ML: 0.5482 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.2344
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2962 731 4.99 %
Rwork0.2389 13914 -
obs0.2416 14645 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.02 Å2
Refinement stepCycle: LAST / Resolution: 3.45→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 60 0 4536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01064668
X-RAY DIFFRACTIONf_angle_d1.29346400
X-RAY DIFFRACTIONf_chiral_restr0.0644750
X-RAY DIFFRACTIONf_plane_restr0.0085826
X-RAY DIFFRACTIONf_dihedral_angle_d14.6167742
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.888427498446 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.720.38651420.3062732X-RAY DIFFRACTION99.79
3.72-4.090.32491450.24472745X-RAY DIFFRACTION99.9
4.09-4.680.251450.21052760X-RAY DIFFRACTION99.9
4.68-5.90.29071470.23382793X-RAY DIFFRACTION99.93
5.9-48.640.2931520.23892884X-RAY DIFFRACTION99.22
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)
18.817566169813.848570215982.064153639244.818109131361.416363223357.59183514911-0.337544442365-0.096040203111-0.303538107032-0.02267411847890.2413577191730.1238694458480.03239157698030.818694415340.1464824740150.624330592509-0.00297999101430.1056545823790.6160059807290.1153961163210.57514954732245.031705109343.0933175317-9.74552488341
2-0.0400406513106-0.56162969190.209861533536.618459036555.704920128548.71794312904-0.2163652714180.5138568281370.745578593036-0.3359220103020.1316335867190.315999633033-0.907072790840.3201853498310.1111704255160.530897767607-0.143407600678-0.02781057075121.118714742430.2474975717880.94031716341245.003968422259.145988603-3.82725312667
36.49633267926-3.507677233442.575519192666.60537211172-0.5091883728963.815626653020.7300805699250.6400244401290.477648827353-2.151678598160.0133079832934-0.64595272364-0.07958332785250.162113253266-0.7605183660581.14280522333-0.2917111784370.1344702683051.28006876306-0.3394863230390.99331816122758.53661565166.10710480785.20859508082
45.3417995273-0.0106498806849-3.526120686826.152998563031.684320267679.09723036750.130288527478-0.770524833970.7700704229090.2196580030430.532150479683-0.536712539690.3391730211410.961661795149-0.6942843495820.86660185518-0.1377413006010.05058687308660.913459287279-0.1772833012270.76136582195247.317787099761.43230258579.22983132804
53.961799594611.315286388484.813806652997.475193945736.697677339719.51790224369-0.129926547578-0.2339910204693.73817733244-3.100624051192.79796462161-1.04365714035-3.010507663534.19740270698-2.401891699841.46062031769-0.6496035992150.3700654668121.95668086226-0.5498082597941.9174180163261.149449950669.5707282732-0.040628171775
67.393396121181.935542363541.923065579251.316521460830.05363618970555.8785436627-0.2568442573180.05239856482080.3629160463930.1179969744820.425497296538-0.273667062271-0.06170398328520.056508499091-0.137700343570.8776554964170.04485473777240.1018771684350.606974332187-0.1469580170030.77546053214234.998861001625.6349126844-16.8486204841
74.489767823681.51472856809-0.07878168746623.59992928596-1.264786366265.16559698288-0.1597009083260.967850978354-0.646147392809-0.5087774270770.15534748358-0.1204754836081.345545151870.699823088894-0.0965753990141.14097787893-0.005206617219870.1227650302570.969036115432-0.2285553020790.76030809900130.813458213410.564131133-19.588875855
84.975465688651.494802022874.202433240022.22863060840.7159730506013.66662523534-1.473011267172.79085298298-4.68846892675-2.010040019731.36051457945-0.5247548241541.84651575481.35599048719-0.6118894335082.36104358206-0.5978546776260.6100007141771.85673731322-0.4258708885782.5011809160231.4438307265-12.4953608671-22.3003643459
98.07033185672-3.45893540329-1.791306954735.9455691413-1.400156858061.81353358140.5040143858180.6424954458361.36753518073-0.615465424446-0.9508603356721.583640427380.0693504474473-0.7460163962560.3168935496542.13669778468-0.387668139355-0.1689073022020.6282660937380.04771290467361.6389177423813.72521262640.034350238993-18.5505046325
102.411887820841.532558724831.658552558084.4749874046-2.922889005545.134956392850.134751182727-0.238052896083-0.0669188107229-0.848627966901-0.908353182997-0.8365223082032.511882115980.07354344590660.3672403289942.412528174820.270629781826-0.06271343795820.5655732931630.01894985742191.1050063446127.7334975655-3.1750280485-14.7381237457
111.544277031660.4170024744460.3290101582793.232913078922.686983224613.022760533980.172291476319-0.01803610472250.3849645103650.301167506439-0.2622967223260.49024474942-0.243724679746-0.2610062899271.275849362612.36339963996-0.819775334698-1.149208281270.42970159922-1.03325013221.3827087868216.2720861958-5.18705768523-27.4623492976
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 174 )AA32 - 1741 - 134
22chain 'A' and (resid 175 through 239 )AA175 - 239135 - 196
33chain 'A' and (resid 240 through 273 )AA240 - 273197 - 230
44chain 'A' and (resid 274 through 399 )AA274 - 399231 - 295
55chain 'A' and (resid 400 through 416 )AA400 - 416296 - 312
66chain 'B' and (resid 33 through 109 )BD33 - 1091 - 77
77chain 'B' and (resid 110 through 229 )BD110 - 22978 - 188
88chain 'B' and (resid 230 through 254 )BD230 - 254189 - 213
99chain 'B' and (resid 255 through 273 )BD255 - 273214 - 232
1010chain 'B' and (resid 274 through 400 )BD274 - 400233 - 287
1111chain 'B' and (resid 401 through 414 )BD401 - 414288 - 301

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