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- PDB-9gnj: Crystal structure of a PP2A B56gamma double phosphorylated BRCA2 ... -

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Basic information

Entry
Database: PDB / ID: 9gnj
TitleCrystal structure of a PP2A B56gamma double phosphorylated BRCA2 complex
Components
  • BRCA2
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


protein phosphatase type 2A complex / meiotic sister chromatid cohesion / 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 ...protein phosphatase type 2A complex / meiotic sister chromatid cohesion / 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 / protein phosphatase activator activity / chromosome, centromeric region / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / Degradation of beta-catenin by the destruction complex / RHO GTPases Activate Formins / RAF activation / 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 / Golgi apparatus / signal transduction / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / Armadillo-like helical / Armadillo-type fold
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 / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMiron, S. / Zinn-Justin, S.
Funding support France, 1items
OrganizationGrant numberCountry
French Alternative Energies and Atomic Energy Commission (CEA) France
CitationJournal: To Be Published
Title: Crystal structure of a PP2A B56gamma double phosphorylated BRCA2 complex
Authors: Miron, S. / Zinn-Justin, S.
History
DepositionSep 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
B: BRCA2


Theoretical massNumber of molelcules
Total (without water)42,9202
Polymers42,9202
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-6 kcal/mol
Surface area17430 Å2
Unit cell
Length a, b, c (Å)53.300, 108.120, 120.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform / PP2A B subunit isoform B'-gamma / PP2A B subunit isoform B56-gamma / PP2A B subunit isoform PR61- ...PP2A B subunit isoform B'-gamma / PP2A B subunit isoform B56-gamma / PP2A B subunit isoform PR61-gamma / PP2A B subunit isoform R5-gamma / Renal carcinoma antigen NY-REN-29


Mass: 41366.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13362
#2: Protein/peptide BRCA2


Mass: 1553.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has ligand of interestY
Has protein modificationY

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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: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% de PEG3350, 100mM Bis-Tris propane, 200 mM de Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.85→49.29 Å / Num. obs: 16827 / % possible obs: 99.82 % / Redundancy: 13.3 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 20.82
Reflection shellResolution: 2.85→2.952 Å / Num. unique obs: 21864 / CC1/2: 0.783

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→49.29 Å / SU ML: 0.4179 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2084 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 842 5.01 %
Rwork0.1967 15975 -
obs0.1984 16817 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 0 0 2825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282901
X-RAY DIFFRACTIONf_angle_d0.51613934
X-RAY DIFFRACTIONf_chiral_restr0.0385436
X-RAY DIFFRACTIONf_plane_restr0.0041492
X-RAY DIFFRACTIONf_dihedral_angle_d13.95691760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.030.36961370.29162603X-RAY DIFFRACTION99.38
3.03-3.260.2821380.27632605X-RAY DIFFRACTION99.89
3.26-3.590.31981380.23152632X-RAY DIFFRACTION99.96
3.59-4.110.26331400.20542660X-RAY DIFFRACTION100
4.11-5.180.19041410.17382670X-RAY DIFFRACTION100
5.18-49.290.19531480.17592805X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: -5.59170418351 Å / Origin y: -14.2590737851 Å / Origin z: 33.7534236305 Å
111213212223313233
T0.461044077258 Å2-0.00797155205109 Å20.0530472930393 Å2-0.551561367796 Å20.0104014198475 Å2--0.609519475875 Å2
L0.449982225858 °20.650117030092 °21.03505671506 °2-4.38631107087 °24.20986339757 °2--5.07291272048 °2
S0.0176736569131 Å °-0.0662061758737 Å °0.176785472801 Å °0.388217133658 Å °-0.128789744837 Å °0.199304764859 Å °0.340318943236 Å °-0.104960623565 Å °0.0617122095481 Å °
Refinement TLS groupSelection details: all

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