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- PDB-3x08: Crystal structure of PIP4KIIBETA N203A complex with GMP -

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Basic information

Entry
Database: PDB / ID: 3x08
TitleCrystal structure of PIP4KIIBETA N203A complex with GMP
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 / GTP binding / endoplasmic reticulum membrane / protein homodimerization activity / nucleoplasm / ATP binding / nucleus / 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 kinases ...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
GUANOSINE-5'-MONOPHOSPHATE / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsTakeuchi, K. / Lo, Y.H. / Sumita, K. / Senda, M. / Terakawa, J. / Dimitoris, A. / Locasale, J.W. / Sasaki, M. / Yoshino, H. / Zhang, Y. ...Takeuchi, K. / Lo, Y.H. / Sumita, K. / Senda, M. / Terakawa, J. / Dimitoris, A. / Locasale, J.W. / Sasaki, M. / Yoshino, H. / Zhang, Y. / Kahoud, E.R. / Takano, T. / Yokota, T. / Emerling, B. / Asara, J.A. / Ishida, T. / Shimada, I. / Daikoku, T. / Cantley, L.C. / Senda, T. / Sasaki, A.T.
CitationJournal: Mol.Cell / Year: 2016
Title: The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Authors: Sumita, K. / Lo, Y.H. / Takeuchi, K. / Senda, M. / Kofuji, S. / Ikeda, Y. / Terakawa, J. / Sasaki, M. / Yoshino, H. / Majd, N. / Zheng, Y. / Kahoud, E.R. / Yokota, T. / Emerling, B.M. / ...Authors: Sumita, K. / Lo, Y.H. / Takeuchi, K. / Senda, M. / Kofuji, S. / Ikeda, Y. / Terakawa, J. / Sasaki, M. / Yoshino, H. / Majd, N. / Zheng, Y. / Kahoud, E.R. / Yokota, T. / Emerling, B.M. / Asara, J.M. / Ishida, T. / Locasale, J.W. / Daikoku, T. / Anastasiou, D. / Senda, T. / Sasaki, A.T.
History
DepositionOct 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)90,8615
Polymers89,7722
Non-polymers1,0903
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-13 kcal/mol
Surface area30660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.381, 182.344, 107.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 44885.879 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 31-416 / Mutation: N203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4K2B / Production host: Escherichia Coli (E. coli)
References: UniProt: P78356, 1-phosphatidylinositol-5-phosphate 4-kinase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 4, 2013
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→92.53 Å / Num. obs: 27463 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 71.68 Å2
Reflection shellResolution: 2.75→2.9 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZZ

3wzz


Resolution: 2.75→91.17 Å / SU ML: 0.5 / σ(F): 0.98 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1379 5.02 %Random
Rwork0.206 ---
obs0.209 27463 98.8 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.22 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 87.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.9397 Å20 Å2-0 Å2
2--1.666 Å20 Å2
3----4.6057 Å2
Refinement stepCycle: LAST / Resolution: 2.75→91.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 72 15 5201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015306
X-RAY DIFFRACTIONf_angle_d1.0837155
X-RAY DIFFRACTIONf_dihedral_angle_d16.4912016
X-RAY DIFFRACTIONf_chiral_restr0.068779
X-RAY DIFFRACTIONf_plane_restr0.004909
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.80010.42191440.36072654100
2.8001-2.85390.37051380.33582665100
2.8539-2.91220.43181370.33952623100
2.9122-2.97550.33551430.28542648100
2.9755-3.04470.34991350.27542632100
3.0447-3.12090.3091410.23212665100
3.1209-3.20530.33391410.23942703100
3.2053-3.29960.24611380.20052617100
3.2996-3.40610.29821380.21222624100
3.4061-3.52780.30351410.21162677100
3.5278-3.66910.25761350.19742635100
3.6691-3.83610.25581420.18682654100
3.8361-4.03830.26971410.1722654100
4.0383-4.29130.21541430.16482662100
4.2913-4.62260.21041400.14522637100
4.6226-5.08780.1921360.14332651100
5.0878-5.82390.2451430.17112645100
5.8239-7.3370.25351400.20272620100
7.337-91.22210.26521120.2126206577
Refinement TLS params.Method: refined / Origin x: 38.4591 Å / Origin y: 31.7482 Å / Origin z: -9.9958 Å
111213212223313233
T0.2615 Å20.0848 Å20.0664 Å2-0.3977 Å20.0023 Å2--0.2178 Å2
L1.6215 °20.5163 °20.4826 °2-1.9849 °21.0454 °2--2.32 °2
S-0.1288 Å °0.1029 Å °-0.1139 Å °-0.0045 Å °0.2659 Å °-0.0853 Å °0.2391 Å °0.5005 Å °-0.0793 Å °
Refinement TLS groupSelection details: ALL

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