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- PDB-2jak: Human PP2A regulatory subunit B56g -

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Basic information

Entry
Database: PDB / ID: 2jak
TitleHuman PP2A regulatory subunit B56g
ComponentsSERINE/THREONINE-PROTEIN PHOSPHATASE 2A 56 KDA REGULATORY SUBUNIT GAMMA ISOFORM
KeywordsNUCLEAR PROTEIN / B56G / PP2A / PPP2R5C / PHOSPHORYLATION / PP2A REGULATORY SUBUNIT
Function / homology
Function and homology information


protein phosphatase type 2A complex / protein phosphatase regulator activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated ...protein phosphatase type 2A complex / protein phosphatase regulator activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Co-stimulation by CD28 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Co-inhibition by CTLA4 / Platelet sensitization by LDL / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein phosphatase activator activity / chromosome, centromeric region / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / DNA damage response, signal transduction by p53 class mediator / RHO GTPases Activate Formins / RAF activation / Degradation of beta-catenin by the destruction complex / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Regulation of TP53 Degradation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of cell population proliferation / signal transduction / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsMagnusdottir, A. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. ...Magnusdottir, A. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lundgren, S. / Moche, M. / Nilsson, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Upsten, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
CitationJournal: Proteins / Year: 2009
Title: The Structure of the Pp2A Regulatory Subunit B56 Gamma: The Remaining Piece of the Pp2A Jigsaw Puzzle.
Authors: Magnusdottir, A. / Stenmark, P. / Flodin, S. / Nyman, T. / Kotenyova, T. / Graslund, S. / Ogg, D. / Nordlund, P.
History
DepositionNov 29, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A 56 KDA REGULATORY SUBUNIT GAMMA ISOFORM


Theoretical massNumber of molelcules
Total (without water)45,8601
Polymers45,8601
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.800, 105.800, 82.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

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Components

#1: Protein SERINE/THREONINE-PROTEIN PHOSPHATASE 2A 56 KDA REGULATORY SUBUNIT GAMMA ISOFORM / PP2A / B SUBUNIT / B' GAMMA ISOFORM / PP2A / B SUBUNIT / B56 GAMMA ISOFORM / PP2A / B SUBUNIT / ...PP2A / B SUBUNIT / B' GAMMA ISOFORM / PP2A / B SUBUNIT / B56 GAMMA ISOFORM / PP2A / B SUBUNIT / PR61 GAMMA ISOFORM / PP2A / B SUBUNIT / R5 GAMMA ISOFORM / NY-REN-29 ANTIGEN / B56G


Mass: 45859.859 Da / Num. of mol.: 1 / Fragment: RESIDUES 11-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13362
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 11-380 WERE EXPRESSED

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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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growDetails: 29% MPD 0.1M TRIS, PH 8.0 20MM L-PROLINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0689
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 7, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0689 Å / Relative weight: 1
ReflectionResolution: 2.6→22 Å / Num. obs: 16638 / % possible obs: 99.7 % / Observed criterion σ(I): 4 / Redundancy: 13.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.11
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 11 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
XDSdata reduction
XSCALEdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→21.47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 24.105 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.415 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 837 5 %RANDOM
Rwork0.214 ---
obs0.216 15799 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0.44 Å20 Å2
2---0.88 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.6→21.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 0 0 17 2693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222750
X-RAY DIFFRACTIONr_bond_other_d0.0020.021870
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9713737
X-RAY DIFFRACTIONr_angle_other_deg0.95134567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6975324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25123.889126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26315469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5231513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02567
X-RAY DIFFRACTIONr_nbd_refined0.2490.2698
X-RAY DIFFRACTIONr_nbd_other0.1870.21857
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21329
X-RAY DIFFRACTIONr_nbtor_other0.090.21335
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0410.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.921706
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3732686
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.92941208
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.72251051
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 66
Rwork0.292 1134
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)
178.2041-21.434745.325432.7614-9.436726.6013-1.60.5308-4.8249-1.01621.2299-0.92191.1692-1.50650.37011.0518-0.10940.17240.69640.11971.0381-0.39616.0528.245
29.09671.1504-0.980411.3257-1.42195.13110.10980.174-1.07290.5256-0.79510.20021.0409-1.29270.68530.3194-0.50870.02340.5844-0.20580.2567-13.22226.2182.964
333.953615.84391.856726.72894.31961.71251.1748-1.9009-0.86733.3221-1.2848-1.61341.1332-0.56950.110.952-0.6552-0.32150.60080.43360.3693-0.99628.3413.798
47.60233.04-1.722416.06213.4197.22310.8116-0.2918-0.4351-0.081-1.4695-0.19750.7797-1.28760.6578-0.1023-0.26820.00460.4297-0.023-0.0583-6.77336.022.325
520.07710.12135.78418.58136.34545.75950.9833-2.0835-0.96971.962-0.8936-1.75921.5356-0.5154-0.08960.1528-0.3639-0.1910.32270.36530.12330.44337.238.857
65.08652.5505-0.792912.29081.81834.48220.316-0.3076-0.3388-0.7609-0.8358-0.38540.1152-0.74350.5198-0.24550.05690.01810.17590.0319-0.1901-2.38149.3310.527
7100.580469.680515.58620.392437.510652.44361.09362.13893.3226-4.9594-3.89741.9632-0.486-1.68422.80380.39350.5197-0.25260.99670.04810.1472-13.17564.269-6.929
82.3508-1.5189-0.817.92484.37634.85420.33920.71050.2007-0.4606-0.73150.3506-0.5662-0.91770.3923-0.14080.1223-0.04640.18850.026-0.1299-5.83271.8549.858
93.01732.7254-0.042512.9244.84094.77520.32070.01940.98760.4326-0.60650.6739-0.2583-1.08310.2857-0.07960.114-0.0032-0.070.03530.0313-8.02684.4324.112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 38
2X-RAY DIFFRACTION2A39 - 73
3X-RAY DIFFRACTION3A74 - 83
4X-RAY DIFFRACTION4A84 - 135
5X-RAY DIFFRACTION5A136 - 151
6X-RAY DIFFRACTION6A152 - 211
7X-RAY DIFFRACTION7A212 - 216
8X-RAY DIFFRACTION8A217 - 340
9X-RAY DIFFRACTION9A341 - 374

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