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- PDB-3fga: Structural Basis of PP2A and Sgo interaction -

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Basic information

Entry
Database: PDB / ID: 3fga
TitleStructural Basis of PP2A and Sgo interaction
Components
  • (Serine/threonine-protein phosphatase 2A ...) x 3
  • MICROCYSTIN-LR
  • Shugoshin-like 1
KeywordsHYDROLASE/hydrolase inhibitor / PP2A / shugoshin / Nucleus / Phosphoprotein / Hydrolase / Iron / Manganese / Metal-binding / Methylation / Protein phosphatase / Cell cycle / Cell division / Centromere / Chromosome partition / Mitosis / HYDROLASE-hydrolase inhibitor complex
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / mitotic sister chromatid cohesion, centromeric / Cyclin A/B1/B2 associated events during G2/M transition / CTLA4 inhibitory signaling / Beta-catenin phosphorylation cascade / centriole-centriole cohesion / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / mitotic sister chromatid cohesion, centromeric / Cyclin A/B1/B2 associated events during G2/M transition / CTLA4 inhibitory signaling / Beta-catenin phosphorylation cascade / centriole-centriole cohesion / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / meiotic spindle elongation / RAF activation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin D associated events in G1 / regulation of microtubule binding / PKR-mediated signaling / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / meiotic chromosome segregation / Degradation of beta-catenin by the destruction complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / DARPP-32 events / attachment of spindle microtubules to kinetochore / peptidyl-serine dephosphorylation / RHO GTPases Activate Formins / peptidyl-threonine dephosphorylation / Separation of Sister Chromatids / positive regulation of microtubule binding / Platelet sensitization by LDL / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Recruitment of NuMA to mitotic centrosomes / ERK/MAPK targets / Anchoring of the basal body to the plasma membrane / female meiotic nuclear division / AURKA Activation by TPX2 / protein antigen binding / meiotic sister chromatid cohesion / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase regulator activity / Regulation of PLK1 Activity at G2/M Transition / GABA receptor binding / condensed chromosome, centromeric region / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / ERKs are inactivated / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / negative regulation of epithelial to mesenchymal transition / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / Platelet sensitization by LDL / protein-serine/threonine phosphatase / regulation of cell differentiation / ERK/MAPK targets / T cell homeostasis / protein phosphatase activator activity / regulation of G1/S transition of mitotic cell cycle / mesoderm development / phosphoprotein phosphatase activity / chromosome, centromeric region / DARPP-32 events / lateral plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / protein dephosphorylation / meiotic cell cycle / protein tyrosine phosphatase activity
Similarity search - Function
Shugoshin, C-terminal / Shugoshin, N-terminal coiled-coil domain / Shugoshin / Shugoshin C terminus / Shugoshin N-terminal coiled-coil region / Single helix bin / Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / HEAT repeat ...Shugoshin, C-terminal / Shugoshin, N-terminal coiled-coil domain / Shugoshin / Shugoshin C terminus / Shugoshin N-terminal coiled-coil region / Single helix bin / Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / HEAT repeat / HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Metallo-dependent phosphatase-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 4-Layer Sandwich / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Microcystin LR / : / : / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform / Shugoshin 1 / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsXu, Z. / Xu, W.
CitationJournal: Mol.Cell / Year: 2009
Title: Structure and function of the PP2A-shugoshin interaction
Authors: Xu, Z. / Cetin, B. / Anger, M. / Cho, U.S. / Helmhart, W. / Nasmyth, K. / Xu, W.
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Jul 27, 2011Group: Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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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 65 kDa regulatory subunit A alpha isoform
B: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
D: Shugoshin-like 1
E: MICROCYSTIN-LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,2747
Polymers155,1645
Non-polymers1102
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-41 kcal/mol
Surface area56230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.940, 145.856, 294.153
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Serine/threonine-protein phosphatase 2A ... , 3 types, 3 molecules ABC

#1: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / PP2A / subunit A / PR65-alpha isoform / PP2A / subunit A / R1-alpha isoform


Mass: 65261.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: PP2A, Ppp2r1a, subunit A / Plasmid: pGEX-6P-1 / Cell line (production host): HI5 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q76MZ3
#2: 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 / Renal carcinoma antigen NY-REN-29


Mass: 47702.367 Da / Num. of mol.: 1 / Fragment: sequence database residues 34-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0044, PP2A, PPP2R5C, subunit B' / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q13362
#3: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 35635.168 Da / Num. of mol.: 1 / Mutation: D88N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PP2A, PPP2CA, subunit c / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P67775, protein-serine/threonine phosphatase

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Protein/peptide , 2 types, 2 molecules DE

#4: Protein/peptide Shugoshin-like 1 / hSgo1 / Serologically defined breast cancer antigen NY-BR-85


Mass: 5551.479 Da / Num. of mol.: 1 / Fragment: sequence database residues 51-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SGO1, SGOL1 / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5FBB7
#5: Protein/peptide MICROCYSTIN-LR


Type: Oligopeptide / Class: Toxin / Mass: 1014.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Microcystis aeruginosa (bacteria) / References: NOR: NOR00109, Microcystin LR

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Non-polymers , 2 types, 94 molecules

#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7
Details: 0.2 M SCTD, 20% w/v Polyethylene glycol 3,350, pH 7, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2008
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 58139 / % possible obs: 92 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.135 / Χ2: 0.995
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.494 / Num. unique all: 3199 / Χ2: 0.869 / % possible all: 51.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.68 Å40.23 Å
Translation2.68 Å40.23 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.03 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.779 / SU B: 12.788 / SU ML: 0.266 / SU R Cruickshank DPI: 0.621 / SU Rfree: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.621 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2898 5 %RANDOM
Rwork0.228 ---
obs0.231 57740 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 111.32 Å2 / Biso mean: 47.846 Å2 / Biso min: 8.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 2 92 10810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210945
X-RAY DIFFRACTIONr_angle_refined_deg1.431.97514840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76951332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.81924.438498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.037151926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2041563
X-RAY DIFFRACTIONr_chiral_restr0.1050.21694
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028187
X-RAY DIFFRACTIONr_nbd_refined0.2340.25311
X-RAY DIFFRACTIONr_nbtor_refined0.3110.27650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2316
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.28
X-RAY DIFFRACTIONr_mcbond_it0.5521.56863
X-RAY DIFFRACTIONr_mcangle_it1.006210868
X-RAY DIFFRACTIONr_scbond_it1.30834542
X-RAY DIFFRACTIONr_scangle_it2.24.53972
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 106 -
Rwork0.307 2239 -
all-2345 -
obs--51.89 %

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