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- PDB-3dw8: Structure of a Protein Phosphatase 2A Holoenzyme with B55 subunit -

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Basic information

Entry
Database: PDB / ID: 3dw8
TitleStructure of a Protein Phosphatase 2A Holoenzyme with B55 subunit
Components
  • Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
  • Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
  • Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • microcystin LR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / holoenzyme / B55 / PR55 / WD repeat / Hydrolase / Iron / Manganese / Metal-binding / Methylation / Phosphoprotein / Protein phosphatase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


regulation of chromosome segregation / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / protein serine/threonine phosphatase complex ...regulation of chromosome segregation / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation / meiotic sister chromatid cohesion, centromeric / INTAC complex / FAR/SIN/STRIPAK complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein phosphatase regulator activity / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / protein antigen binding / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / 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 / RNA polymerase II transcription initiation surveillance / Co-stimulation by CD28 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of epithelial to mesenchymal transition / response to morphine / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / ERK/MAPK targets / protein serine/threonine phosphatase activity / mesoderm development / vascular endothelial cell response to oscillatory fluid shear stress / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / regulation of cell differentiation / regulation of microtubule polymerization / phosphoprotein phosphatase activity / lateral plasma membrane / chromosome, centromeric region / DARPP-32 events / enzyme-substrate adaptor activity / negative regulation of hippo signaling / Cyclin A/B1/B2 associated events during G2/M transition / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein dephosphorylation / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein tyrosine phosphatase activity / Resolution of Sister Chromatid Cohesion / protein phosphatase 2A binding / AURKA Activation by TPX2 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Spry regulation of FGF signaling / meiotic cell cycle / chromosome segregation / Degradation of beta-catenin by the destruction complex / RAF activation / RHO GTPases Activate Formins / negative regulation of canonical Wnt signaling pathway / PKR-mediated signaling / tau protein binding / response to lead ion / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / microtubule cytoskeleton / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / neuron projection / intracellular signal transduction / membrane raft
Similarity search - Function
Protein phosphatase 2A regulatory subunit PR55 / Protein phosphatase 2A regulatory subunit PR55, conserved site / Protein phosphatase 2A regulatory subunit PR55 signature 1. / Protein phosphatase 2A regulatory subunit PR55 signature 2. / : / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat ...Protein phosphatase 2A regulatory subunit PR55 / Protein phosphatase 2A regulatory subunit PR55, conserved site / Protein phosphatase 2A regulatory subunit PR55 signature 1. / Protein phosphatase 2A regulatory subunit PR55 signature 2. / : / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like 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 / Metallo-dependent phosphatase-like / Leucine-rich Repeat Variant / 4-Layer Sandwich / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Microcystin LR / : / : / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
Cyanobacteria (blue-green algae)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsXu, Y. / Chen, Y. / Zhang, P. / Jeffrey, P.D. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2008
Title: Structure of a protein phosphatase 2A holoenzyme: insights into B55-mediated Tau dephosphorylation.
Authors: Xu, Y. / Chen, Y. / Zhang, P. / Jeffrey, P.D. / Shi, Y.
History
DepositionJul 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Sep 25, 2013Group: Derived calculations
Revision 1.5Oct 16, 2013Group: Derived calculations
Revision 1.6Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 / pdbx_validate_rmsd_angle / 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
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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 55 kDa regulatory subunit B alpha isoform
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
D: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
E: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
F: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
G: microcystin LR
H: microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,54212
Polymers306,3228
Non-polymers2204
Water00
1
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
B: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
G: microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,2716
Polymers153,1614
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-40 kcal/mol
Surface area53800 Å2
MethodPISA
2
D: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
E: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
F: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
H: microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,2716
Polymers153,1614
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-37 kcal/mol
Surface area53730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.340, 121.390, 172.480
Angle α, β, γ (deg.)90.00, 132.60, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a heterotrimer. There are two biological units in the asymmetric unit: first heterotrimer consisting of polypeptide chains A,B,C corresponding to PP2A subunits bound to catalytic MN atoms and MCLR inhibitor (chain G), and second heterotrimer consisting of polypeptide chains D,E,F corresponding to PP2A subunits bound to catalytic MN atoms and MCLR inhibitor (chain H).

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Components

#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 / Medium tumor antigen- ...PP2A / subunit A / PR65-alpha isoform / PP2A / subunit A / R1-alpha isoform / Medium tumor antigen-associated 61 kDa protein


Mass: 64762.785 Da / Num. of mol.: 2 / Fragment: A delta 8: Residues 9-589
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Production host: Escherichia coli (E. coli) / References: UniProt: P30153
#2: Protein Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform / PP2A / subunit B / B-alpha isoform / PP2A / subunit B / B55-alpha isoform / PP2A / subunit B / PR55- ...PP2A / subunit B / B-alpha isoform / PP2A / subunit B / B55-alpha isoform / PP2A / subunit B / PR55-alpha isoform / PP2A / subunit B / R2-alpha isoform


Mass: 51747.984 Da / Num. of mol.: 2 / Mutation: I310V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R2A / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63151
#3: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 35636.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P67775, protein-serine/threonine phosphatase
#4: Protein/peptide microcystin LR


Type: Oligopeptide / Class: Toxin / Mass: 1014.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Cyanobacteria (blue-green algae) / References: NOR: NOR00109, Microcystin LR
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 7-10% PEG 35000, 0.10-0.15 M Sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.85→100 Å / Num. all: 87353 / Num. obs: 87353 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 65.9 Å2
Reflection shellResolution: 2.85→2.95 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PP2A A subunit, PP2A C subunit, WD40 ensemble

Resolution: 2.85→49.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2550770.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 4180 5 %RANDOM
Rwork0.228 ---
all0.231 83615 --
obs0.231 83615 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.0084 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 93.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å210.54 Å2
2--2.24 Å20 Å2
3----5.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.85→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20713 0 4 0 20717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 525 4.9 %
Rwork0.335 10100 -
obs--73.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2mclr_composite2.parmclr_composite2.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4ion.paramtopo_mn.inp
X-RAY DIFFRACTION5param_mn.inp

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