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- PDB-3c5w: Complex between PP2A-specific methylesterase PME-1 and PP2A core ... -

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Basic information

Entry
Database: PDB / ID: 3c5w
TitleComplex between PP2A-specific methylesterase PME-1 and PP2A core enzyme
Components
  • PP2A A subunit
  • PP2A C subunit
  • PP2A-specific methylesterase PME-1
KeywordsHYDROLASE / methylesterase / phosphatase / PP2A
Function / homology
Function and homology information


protein phosphatase methylesterase-1 / : / 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 ...protein phosphatase methylesterase-1 / : / 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 / 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 / protein phosphatase inhibitor activity / Platelet sensitization by LDL / protein-serine/threonine phosphatase / negative regulation of glycolytic process through fructose-6-phosphate / lncRNA binding / 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 / lateral plasma membrane / chromosome, centromeric region / DARPP-32 events / 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 / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AURKA Activation by TPX2 / meiotic cell cycle / chromosome segregation / RHO GTPases Activate Formins / Spry regulation of FGF signaling / RAF activation / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / response to lead ion / G2/M transition of mitotic cell cycle / 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 / protein phosphatase binding
Similarity search - Function
Protein phosphatase methylesterase, eukaryotic / : / : / HEAT repeat / HEAT repeat / Lipases, serine active site. / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. ...Protein phosphatase methylesterase, eukaryotic / : / : / HEAT repeat / HEAT repeat / Lipases, serine active site. / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Alpha/beta hydrolase family / 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 / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / 4-Layer Sandwich / Armadillo-like helical / Alpha Horseshoe / Alpha/Beta hydrolase fold / Armadillo-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Protein phosphatase methylesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXing, Y. / Li, Z. / Chen, Y. / Stock, J. / Jeffrey, P.D. / Shi, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural mechanism of demethylation and inactivation of protein phosphatase 2A.
Authors: Xing, Y. / Li, Z. / Chen, Y. / Stock, J.B. / Jeffrey, P.D. / Shi, Y.
History
DepositionFeb 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 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: PP2A A subunit
C: PP2A C subunit
P: PP2A-specific methylesterase PME-1


Theoretical massNumber of molelcules
Total (without water)95,6773
Polymers95,6773
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.292, 54.839, 125.146
Angle α, β, γ (deg.)90.00, 110.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PP2A A subunit


Mass: 25896.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P30153
#2: Protein PP2A C subunit


Mass: 35693.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P67775
#3: Protein PP2A-specific methylesterase PME-1


Mass: 34087.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y570
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A HAS 47-399 RESIDUES DELETION AND CHAIN P HAS 239-283 LOOP REPLACED BY EGK. THE PROTEIN ...CHAIN A HAS 47-399 RESIDUES DELETION AND CHAIN P HAS 239-283 LOOP REPLACED BY EGK. THE PROTEIN CONSTRUCT (CHAIN P) IS A NON-CATALYTIC MUTANT WITH SER156 REPLACED BY ALA.

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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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% w/v PEG3350, 100 mM ammonium citrate, and 5 mM DTT, pH 7.5, 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: Sep 10, 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: 2.8→100 Å / Num. all: 20623 / Num. obs: 20623 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rsym value: 0.095
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rsym value: 0.4 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0038refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PP2A A subunit, PP2A C subunit, PME-1 monomer

Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.874 / SU B: 34.63 / SU ML: 0.325 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26338 1018 5 %RANDOM
Rwork0.19513 ---
obs0.19844 19235 98.63 %-
all-19235 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.744 Å2
Baniso -1Baniso -2Baniso -3
1--3.32 Å20 Å2-1.39 Å2
2--1.39 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6441 0 0 62 6503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226579
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.9648922
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1235811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02924.276297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.005151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.991539
X-RAY DIFFRACTIONr_chiral_restr0.0720.21005
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024950
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.23244
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24503
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2491.54175
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.44526557
X-RAY DIFFRACTIONr_scbond_it0.63332730
X-RAY DIFFRACTIONr_scangle_it1.0494.52365
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 76 -
Rwork0.246 1356 -
obs--95.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.0328-2.4129-2.10946.96770.42516.90440.37820.0349-0.18890.2988-0.2210.93520.9379-0.2054-0.15730.3270.08370.04980.4444-0.06870.1794-35.94612.17842.6351
210.5488-2.008-4.45431.08251.70187.2277-0.5512-0.72350.7518-0.25930.38570.9387-0.4504-0.36270.1655-0.0857-0.0145-0.0566-0.05940.07780.3068-34.47042.992428.3509
34.41060.3187-2.63851.6241-0.68082.2941-0.35091.2696-0.3582-0.59320.17470.55160.2963-0.76570.17630.0515-0.2975-0.03790.30310.0178-0.1483-28.0487-8.72617.2781
43.11650.4031-0.15171.8864-0.2952.486-0.05110.242-0.1052-0.07340.0574-0.06690.30410.0489-0.0063-0.2067-0.04940.0212-0.2771-0.0078-0.27871.5805-2.899920.9402
52.3233-0.96540.77632.6104-1.86433.7488-0.1714-0.19430.02320.4565-0.1691-0.4014-0.35890.45430.3405-0.1149-0.0943-0.0792-0.0634-0.0248-0.099623.61251.221852.5886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 465 - 42
2X-RAY DIFFRACTION2AA402 - 45445 - 97
3X-RAY DIFFRACTION3AA455 - 58998 - 232
4X-RAY DIFFRACTION4CB6 - 2937 - 294
5X-RAY DIFFRACTION5PC39 - 3765 - 300
6X-RAY DIFFRACTION5CB304 - 309305 - 310

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