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- PDB-3x04: Crystal structure of PIP4KIIBETA complex with GMPPNP -

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Basic information

Entry
Database: PDB / ID: 3x04
TitleCrystal structure of PIP4KIIBETA complex with GMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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)91,9476
Polymers89,8582
Non-polymers2,0894
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-21 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.804, 185.222, 106.449
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: 44928.902 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 31-416
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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
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: Mar 11, 2012
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→94.454 Å / Num. obs: 33027 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 70.82 Å2
Reflection shellResolution: 2.6→2.74 Å / % possible all: 99.8

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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: 2.6→94.45 Å / SU ML: 0.56 / σ(F): 1.18 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1648 4.99 %Random
Rwork0.229 ---
obs0.231 33027 97.9 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.42 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 84.34 Å2
Baniso -1Baniso -2Baniso -3
1-3.4789 Å20 Å2-0 Å2
2--0.3688 Å20 Å2
3----3.8477 Å2
Refinement stepCycle: LAST / Resolution: 2.6→94.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5035 0 120 17 5172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015272
X-RAY DIFFRACTIONf_angle_d1.2367124
X-RAY DIFFRACTIONf_dihedral_angle_d16.6871996
X-RAY DIFFRACTIONf_chiral_restr0.076772
X-RAY DIFFRACTIONf_plane_restr0.005894
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6001-2.63890.53341430.47062672100
2.6389-2.68020.47541410.47062675100
2.6802-2.72410.66561360.46972623100
2.7241-2.77110.44211370.39542693100
2.7711-2.82150.42961420.37672643100
2.8215-2.87570.40971340.3342660100
2.8757-2.93450.2941390.32962672100
2.9345-2.99830.40761380.28452655100
2.9983-3.0680.3431390.26962659100
3.068-3.14470.26551400.24822675100
3.1447-3.22980.30031410.23322652100
3.2298-3.32480.27761380.23372680100
3.3248-3.43210.2951420.22222670100
3.4321-3.55480.33881430.23272635100
3.5548-3.69710.30671410.2692263899
3.6971-3.86540.2371400.22182632100
3.8654-4.06920.23421420.1962265099
4.0692-4.32410.21461340.1814265099
4.3241-4.6580.24281400.15652659100
4.658-5.12670.17251380.1486264099
5.1267-5.86850.21471400.1682264699
5.8685-7.39320.2841350.1919262298
7.3932-94.51620.2341880.2285162461
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)
17.83290.44071.69213.67040.80314.6194-0.25120.1814-0.21-0.21480.6163-0.08390.09530.57-0.30940.3-0.05390.08860.4521-0.07090.273242.765338.655-12.5932
28.602-0.3782-0.645.79561.27826.1438-0.3812-0.45570.38990.16060.46080.4042-0.09270.2497-0.1210.3328-0.00750.04930.4579-0.05010.385341.111547.4061-2.2945
33.32760.0049-0.00443.79861.76993.2038-0.45090.42840.6308-0.33940.6451-0.3566-0.20721.2149-0.20080.3658-0.22690.12950.6663-0.08140.374751.178551.0588-7.1661
47.35251.1008-1.44065.84350.34548.6319-0.4870.37692.1122-0.71750.67750.4423-1.63790.3166-0.22080.7675-0.1378-0.04560.5240.01730.95147.367173.13311.5211
54.849-0.3082-3.63434.0051-0.28996.5171-0.53051.0977-0.0064-0.47330.6256-0.90560.12030.4707-0.03510.3902-0.29410.08761.0609-0.27070.757363.169960.73040.1194
67.75780.2049-1.99485.11461.08246.7122-0.284-0.31840.94940.42340.6326-0.3725-0.2860.3978-0.25870.4173-0.0166-0.02390.4122-0.16290.569149.568763.01138.9618
76.48162.6305-1.48323.07220.19935.24760.0230.1803-0.1042-0.18650.2678-0.303-0.18090.6676-0.25390.32440.03050.02790.3159-0.09050.266835.439325.6501-17.1144
87.63940.22972.16572.9701-0.69655.9879-0.12620.4822-0.6585-0.28560.17860.1110.49310.2374-0.06010.5986-0.03440.00830.2822-0.11640.450230.242613.8197-17.625
92.4698-0.39250.09833.81430.1862.4566-0.1120.611-1.12-0.62120.50870.18131.4960.173-0.08461.099-0.0512-0.09610.4511-0.33550.666827.85930.1888-21.7005
100.94680.1196-1.52563.8796-0.37312.70490.43530.4802-1.0299-1.17610.0660.34351.8443-0.3225-0.34541.4707-0.1176-0.39720.3194-0.24141.012325.0174-4.9424-16.5916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 33:109)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 110:153)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 154:212)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 213:253)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 254:279)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 280:416)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 33:109)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 110:173)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 174:273)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 274:416)

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