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- PDB-7em8: Crystal structure of the PI5P4Kbeta T201M-2a-ATP complex -

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Basic information

Entry
Database: PDB / ID: 7em8
TitleCrystal structure of the PI5P4Kbeta T201M-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 / autophagosome / negative regulation of insulin receptor signaling pathway / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell surface receptor signaling pathway / phosphorylation / endoplasmic reticulum membrane / GTP binding / protein homodimerization activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
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
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: 3.05 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)90,8824
Polymers89,9182
Non-polymers9642
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-11 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.487, 184.854, 106.735
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
14GLYGLYLEULEU(chain 'A' and ((resid 33 and (name N or name...AA338 - 371315 - 348
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
29GLYGLYLEULEU(chain 'B' and (resid 33 through 64 or (resid 65...BB338 - 371315 - 348
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 / PI(5)P 4-kinase type II beta / PIP4KII-beta / PtdIns(5)P-4-kinase isoform 2-beta


Mass: 44958.996 Da / Num. of mol.: 2 / Mutation: T201M
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 Å3/Da / Density % sol: 59.04 %
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

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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: Mar 1, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.05→47.97 Å / Num. obs: 21000 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 95.96 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.15
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.909 / Num. unique obs: 2938 / % 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: 3.05→46.22 Å / SU ML: 0.383 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.9141
RfactorNum. reflection% reflection
Rfree0.2747 1048 4.99 %
Rwork0.2092 --
obs0.2124 20989 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 101.18 Å2
Refinement stepCycle: LAST / Resolution: 3.05→46.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4605 0 60 0 4665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00984770
X-RAY DIFFRACTIONf_angle_d1.19616514
X-RAY DIFFRACTIONf_chiral_restr0.0729754
X-RAY DIFFRACTIONf_plane_restr0.007840
X-RAY DIFFRACTIONf_dihedral_angle_d6.51752860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.210.30971470.28742802X-RAY DIFFRACTION100
3.21-3.410.32791460.25832791X-RAY DIFFRACTION99.93
3.41-3.680.24711500.23032842X-RAY DIFFRACTION100
3.68-4.040.28921480.19812816X-RAY DIFFRACTION100
4.04-4.630.25091500.17342856X-RAY DIFFRACTION100
4.63-5.830.24521510.19822873X-RAY DIFFRACTION100
5.83-46.220.29391560.21482961X-RAY DIFFRACTION99.43
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)
16.493227311532.248608373372.857611534674.123772535011.120358135813.67894807865-0.06393683971040.289085183094-0.0975527390455-0.3834689150940.2413911249750.09776373328920.22656878290.655775619405-0.1299039845180.5438902244010.05387114205050.1248802193230.7302223133440.09122875846070.46595119364542.423068508738.3588274804-12.7714786649
29.482959923542.50566730935-1.705448922642.040582057770.8310112604938.66644582582-0.104697403112-0.7788876862220.5956861772940.1830646927530.1363630736110.4549422078080.0790535606482-0.4374857826480.01519526473120.5997334680210.08281078707690.04255469570460.586247352397-0.110443573070.71803196940441.001688094347.3368315457-2.64807496158
35.56676442239-0.0873744057046-0.1039026082516.212864391663.568337682684.61271559676-0.344019975376-0.05850014623181.035012231190.02906549736760.696104052930.0371653770393-0.08715649406771.01297992713-0.4122647198030.436028187025-0.1015616570510.04105585892040.6252491698450.04354289608750.62612214828750.272047937252.3277293957-6.54894244612
42.480674537931.041702174520.7504729637597.535857913881.114102100511.98310070468-0.3330024370150.7553447727073.26184085868-0.3980822259860.4062581170490.26603900435-1.895186740780.913275265986-0.1883219316151.04838237125-0.07865138540110.03503529237981.304737622710.3159983227361.6162917859546.556045932373.5326998822.23109139608
58.35105613410.142448631057-0.6751013721753.341945820412.058611358885.64914436932-1.032813205690.02450954348330.409526484190.1473923932730.316453714664-0.02230657532550.516050601156-0.2377174728020.5805825086050.8091694309960.02420023885290.09701618068280.536721414896-0.1942922008621.0762919671852.048527747561.60911913696.7082861492
65.149822704-0.391101366212-0.8110474610163.483853988372.088566227713.275346827370.106621033696-0.9117771744221.884183332380.1479192461540.335203838401-0.0612867434664-0.5246320133370.613736595019-0.540862108380.648786642229-0.001955914199110.007046557206080.736961165134-0.3477311136331.216062163354.368127503362.69863452596.07282303581
76.061110942371.325295325890.1768011101713.035477947560.6751688360132.360887852170.05402713319430.2689814802590.0645257645775-0.1333793621340.183267950626-0.140445331105-0.1114184282630.278280168382-0.2098042401390.6584016798540.03043173977170.06897374363460.533951273374-0.05817548285560.44247889735634.913159828625.3674569593-17.2302639046
86.615197359130.5273073953853.710814968575.14755087327-4.005183555.926917617230.4522213893210.2795444765520.00198850261705-0.038917814869-0.194673195119-0.2003403848170.6208812478770.571284699116-0.2373544331530.8683788326040.06335827691180.01895653836730.519100896495-0.02711070274180.66019379767436.466396744412.3897709917-14.1601141307
93.715730150750.879867952452-0.03003686469547.755041814090.2690549399574.179896946640.007977917434950.813737657067-0.45424299591-0.6763132371810.3783423752350.4296906619580.7475820022970.289535612106-0.2951732675330.700417632757-0.069004826445-0.1092675898990.690293352575-0.09980630910360.51874238957427.49885784169.38059556065-21.8167061103
108.192221281-0.6168671389190.1388557520534.36740584234-2.550383808721.48504934459-0.1433018376221.49934667366-2.27875306543-1.69751879145-0.03662859189560.8752475568960.6600532651010.3566350739440.1855021202211.81132193232-0.149165296084-0.06730390383170.973559621442-0.3893503712231.3992774542222.6072950297-6.84442381344-20.4597626181
112.008722146351.23614307658-0.586063928232.857442551811.645368577012.073392185380.618483563309-0.111733770017-0.684490656288-0.436232405922-0.039699171720.7134212592281.868520104230.125285488194-0.5430938738081.59226837231-0.0448961640583-0.2813669266230.525528330548-0.06631952281751.102019331625.5439927869-4.8359636184-15.7281196716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 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 229 )
10X-RAY DIFFRACTION10chain 'B' and (resid 230 through 273 )
11X-RAY DIFFRACTION11chain 'B' and (resid 274 through 415 )

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