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- PDB-3x06: Crystal structure of PIP4KIIBETA T201M complex with GMP -

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Basic information

Entry
Database: PDB / ID: 3x06
TitleCrystal structure of PIP4KIIBETA T201M 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: 2.65 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)91,7347
Polymers89,9182
Non-polymers1,8165
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-17 kcal/mol
Surface area30180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.825, 182.878, 106.657
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: 44958.996 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 31-416 / Mutation: T201M
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.: 5 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
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: Jan 20, 2013
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→91.44 Å / Num. obs: 30962 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 68.21 Å2
Reflection shellResolution: 2.65→2.79 Å / % possible all: 99.5

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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: 2.65→54.41 Å / SU ML: 0.51 / σ(F): 1.35 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1536 4.96 %Random
Rwork0.212 ---
obs0.214 30962 99 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.89 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 81.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.2429 Å20 Å2-0 Å2
2--1.1391 Å20 Å2
3----2.382 Å2
Refinement stepCycle: LAST / Resolution: 2.65→54.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5113 0 120 31 5264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115367
X-RAY DIFFRACTIONf_angle_d1.1127242
X-RAY DIFFRACTIONf_dihedral_angle_d17.552041
X-RAY DIFFRACTIONf_chiral_restr0.068784
X-RAY DIFFRACTIONf_plane_restr0.005914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6501-2.69350.4381380.4149264599
2.6935-2.740.39591420.3636272799
2.74-2.78980.41531410.35052704100
2.7898-2.84340.37911370.3077264499
2.8434-2.90150.41651430.3269269299
2.9015-2.96460.35771450.27232707100
2.9646-3.03350.2581400.24592698100
3.0335-3.10940.33921450.24072682100
3.1094-3.19340.3331360.22862700100
3.1934-3.28740.2551400.21022687100
3.2874-3.39350.27471380.21082700100
3.3935-3.51470.27031430.21052722100
3.5147-3.65540.28341390.21252698100
3.6554-3.82180.26621440.1952691100
3.8218-4.02320.2031390.18672673100
4.0232-4.27520.23091420.1663270599
4.2752-4.60510.19081400.15582705100
4.6051-5.06820.21311460.1422702100
5.0682-5.80090.20631350.17042688100
5.8009-7.30570.24211410.21352691100
7.3057-54.42390.2521190.2053234286
Refinement TLS params.Method: refined / Origin x: 38.7378 Å / Origin y: 31.6038 Å / Origin z: -10.0614 Å
111213212223313233
T0.2355 Å20.0441 Å20.0591 Å2-0.4001 Å20.0047 Å2--0.1842 Å2
L1.7429 °20.7378 °20.6884 °2-2.7361 °21.2299 °2--2.0732 °2
S-0.1515 Å °0.1727 Å °-0.0838 Å °-0.0179 Å °0.3046 Å °-0.1043 Å °0.1763 Å °0.4217 Å °-0.11 Å °
Refinement TLS groupSelection details: ALL

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