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- PDB-3x0c: Crystal structure of PIP4KIIBETA I368A complex with GMP -

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Basic information

Entry
Database: PDB / ID: 3x0c
TitleCrystal structure of PIP4KIIBETA I368A 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 / negative regulation of insulin receptor signaling pathway / autophagosome / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 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 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: 2.55 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)91,2276
Polymers89,7742
Non-polymers1,4534
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-21 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.102, 183.392, 106.536
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: 44886.824 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 31-416 / Mutation: I368A
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


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
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: Dec 2, 2012
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→93.76 Å / Num. obs: 34600 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 65.38 Å2
Reflection shellResolution: 2.55→2.69 Å / % possible all: 99

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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: 2.55→54.55 Å / SU ML: 0.49 / σ(F): 1.41 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1740 5.03 %Random
Rwork0.223 ---
obs0.225 34600 98.3 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.42 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 80.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.9049 Å20 Å2-0 Å2
2---0.5005 Å20 Å2
3----2.4044 Å2
Refinement stepCycle: LAST / Resolution: 2.55→54.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5127 0 96 42 5265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115329
X-RAY DIFFRACTIONf_angle_d1.1467193
X-RAY DIFFRACTIONf_dihedral_angle_d16.2762023
X-RAY DIFFRACTIONf_chiral_restr0.072782
X-RAY DIFFRACTIONf_plane_restr0.005911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.58640.40481420.3922264199
2.5864-2.6250.5061380.4145261799
2.625-2.66610.46141450.4032266799
2.6661-2.70980.43941380.3998262199
2.7098-2.75650.41631370.3325260899
2.7565-2.80660.31861440.2736268699
2.8066-2.86060.3071350.2843258499
2.8606-2.9190.34871390.3027265499
2.919-2.98240.33791450.27265399
2.9824-3.05180.32831410.2483265399
3.0518-3.12810.31611410.2362264599
3.1281-3.21270.31061370.2362262599
3.2127-3.30720.27971400.2405267399
3.3072-3.41390.30131410.22622647100
3.4139-3.53590.2691390.22322652100
3.5359-3.67750.24731400.21422656100
3.6775-3.84480.23891420.19772648100
3.8448-4.04750.24551380.1857263199
4.0475-4.3010.23591390.1683264699
4.301-4.63290.23891430.15122654100
4.6329-5.09880.21711410.15972667100
5.0988-5.83590.20041390.17162647100
5.8359-7.34970.19331410.19772649100
7.3497-54.56350.29471080.21206977
Refinement TLS params.Method: refined / Origin x: 38.8444 Å / Origin y: 31.5323 Å / Origin z: -10.2806 Å
111213212223313233
T0.222 Å20.0522 Å20.0641 Å2-0.4032 Å2-0.0191 Å2--0.1742 Å2
L1.896 °20.9829 °20.8015 °2-2.645 °21.1363 °2--2.0012 °2
S-0.1583 Å °0.2551 Å °-0.0845 Å °0.0166 Å °0.334 Å °-0.0322 Å °0.1813 Å °0.4332 Å °-0.1071 Å °
Refinement TLS groupSelection details: ALL

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