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- PDB-5sw9: The structure of the PP2A B56 subunit RepoMan complex -

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Basic information

Entry
Database: PDB / ID: 5sw9
TitleThe structure of the PP2A B56 subunit RepoMan complex
Components
  • RepoMan
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
KeywordsHydrolase / cell cycle / Phosphatase / Regulator / SLiM
Function / homology
Function and homology information


regulation of chromosome segregation / 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 ...regulation of chromosome segregation / 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 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of mitotic nuclear division / Platelet sensitization by LDL / CTLA4 inhibitory signaling / 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 / : / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Resolution of Sister Chromatid Cohesion / chromosome segregation / 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 / chromosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of cell population proliferation / cell division / Golgi apparatus / signal transduction / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein phosphatase 1 binding domain / Protein phosphatase 1 binding / Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform / Cell division cycle-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.846 Å
AuthorsPage, R. / Wang, X. / Bajaj, R. / Peti, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS091336 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098482 United States
CitationJournal: Structure / Year: 2016
Title: Expanding the PP2A Interactome by Defining a B56-Specific SLiM.
Authors: Wang, X. / Bajaj, R. / Bollen, M. / Peti, W. / Page, R.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: RepoMan


Theoretical massNumber of molelcules
Total (without water)44,0792
Polymers44,0792
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-8 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.598, 108.959, 120.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 41667.219 Da / Num. of mol.: 1 / Fragment: UNP residues 62-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13362
#2: Protein/peptide RepoMan


Mass: 2411.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q69YH5*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.75 / Details: 8% PEG 8K, 0.8 M HEPES, 0.8 M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.846→38.207 Å / Num. obs: 16968 / % possible obs: 99.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 13
Reflection shellResolution: 2.85→3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 2 / CC1/2: 0.686 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5K6S

5k6s


Resolution: 2.846→38.207 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 1694 9.98 %
Rwork0.1984 --
obs0.2013 16968 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.846→38.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 0 23 2791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022846
X-RAY DIFFRACTIONf_angle_d0.6543868
X-RAY DIFFRACTIONf_dihedral_angle_d12.0291059
X-RAY DIFFRACTIONf_chiral_restr0.023430
X-RAY DIFFRACTIONf_plane_restr0.004488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8462-2.92990.36331380.30961204X-RAY DIFFRACTION96
2.9299-3.02440.32061390.28561237X-RAY DIFFRACTION99
3.0244-3.13250.3281370.27611266X-RAY DIFFRACTION99
3.1325-3.25780.31071350.26171252X-RAY DIFFRACTION100
3.2578-3.4060.29481440.23441269X-RAY DIFFRACTION99
3.406-3.58550.28871350.20751275X-RAY DIFFRACTION100
3.5855-3.80990.23641470.1931261X-RAY DIFFRACTION100
3.8099-4.10380.21831360.18651272X-RAY DIFFRACTION100
4.1038-4.51610.19411460.16041285X-RAY DIFFRACTION100
4.5161-5.16830.19981390.16541283X-RAY DIFFRACTION100
5.1683-6.50630.18731480.19691307X-RAY DIFFRACTION100
6.5063-38.21080.17871500.17771363X-RAY DIFFRACTION98

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