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- PDB-2nyl: Crystal structure of Protein Phosphatase 2A (PP2A) holoenzyme wit... -

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Entry
Database: PDB / ID: 2nyl
TitleCrystal structure of Protein Phosphatase 2A (PP2A) holoenzyme with the catalytic subunit carboxyl terminus truncated
Components
  • Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
  • Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • microcystin LR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HEAT repeat / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation ...meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation / mitotic sister chromatid separation / meiotic sister chromatid cohesion, centromeric / INTAC complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / meiotic sister chromatid cohesion / 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 / 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 / Initiation of Nuclear Envelope (NE) Reformation / 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 / 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 / mesoderm development / protein serine/threonine phosphatase activity / vascular endothelial cell response to oscillatory fluid shear stress / T cell homeostasis / regulation of cell differentiation / phosphoprotein phosphatase activity / regulation of microtubule polymerization / regulation of G1/S transition of mitotic cell cycle / protein phosphatase activator activity / lateral plasma membrane / chromosome, centromeric region / DARPP-32 events / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of hippo signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein dephosphorylation / Cyclin A/B1/B2 associated events during G2/M transition / 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 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AURKA Activation by TPX2 / meiotic cell cycle / chromosome segregation / DNA damage response, signal transduction by p53 class mediator / RHO GTPases Activate Formins / RAF activation / Spry regulation of FGF signaling / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / response to lead ion / tau protein binding / spindle pole / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron projection / intracellular signal transduction
Similarity search - Function
Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. ...Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / : / 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 / Metallo-dependent phosphatases / HEAT repeats / 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 / 4-Layer Sandwich / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / 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 catalytic subunit alpha isoform / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
Cyanobacteria (cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsXing, Y. / Xu, Y. / Chen, Y. / Chao, Y. / Lin, Z. / Shi, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structure of the Protein Phosphatase 2A Holoenzyme.
Authors: Xu, Y. / Xing, Y. / Chen, Y. / Chao, Y. / Lin, Z. / Fan, E. / Yu, J.W. / Strack, S. / Jeffrey, P.D. / Shi, Y.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Feb 27, 2013Group: Other
Revision 1.5Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.6Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase 2, regulatory subunit A (PR 65), 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: Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform
E: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma 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)293,24512
Polymers293,0258
Non-polymers2204
Water00
1
A: Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform
B: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
G: microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,6236
Polymers146,5134
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform
E: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
F: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
H: microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,6236
Polymers146,5134
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.480, 159.850, 270.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsEach holoenzyme contains one copy of catalytic subunit, one copy of scaffolding subunit and one copy of the regulatory subunit.

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Components

#1: Protein Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform


Mass: 65356.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96DH3, UniProt: P30153*PLUS
#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 / NY-REN-29 antigen


Mass: 46467.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13362
#3: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 33674.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5
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 (cyanobacteria) / 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: 4.04 Å3/Da / Density % sol: 69.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10-15% PEG8000, 0.1 M Tris-Cl, 0.2 M magnesium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.8→100 Å / Num. all: 47152 / Num. obs: 45951 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.109 / Χ2: 1.362 / Net I/σ(I): 9.3
Reflection shellResolution: 3.8→3.94 Å / Rmerge(I) obs: 0.432 / Num. unique all: 4521 / Χ2: 0.781 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NPP

2npp


Resolution: 3.8→100 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.335 2361 5 %
Rwork0.282 --
all0.32 --
obs0.3 46983 99.6 %
Solvent computationBsol: 116.738 Å2
Displacement parametersBiso mean: 80.556 Å2
Baniso -1Baniso -2Baniso -3
1--12.632 Å20 Å20 Å2
2---33.815 Å20 Å2
3---46.448 Å2
Refinement stepCycle: LAST / Resolution: 3.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20208 0 4 0 20212
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.558
X-RAY DIFFRACTIONc_mcbond_it2.4381.5
X-RAY DIFFRACTIONc_scbond_it3.3972
X-RAY DIFFRACTIONc_mcangle_it4.3282
X-RAY DIFFRACTIONc_scangle_it5.6362.5
LS refinement shellResolution: 3.8→3.94 Å
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2param_mn.inpdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5mclr_composite2.par

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