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- PDB-3k7w: Protein phosphatase 2A core complex bound to dinophysistoxin-2 -

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Basic information

Entry
Database: PDB / ID: 3k7w
TitleProtein phosphatase 2A core complex bound to dinophysistoxin-2
Components(Serine/threonine-protein phosphatase 2A ...) x 2
KeywordsSIGNALING PROTEIN/HYDROLASE / PROTEIN-PROTEIN COMPLEX / HEAT REPEAT / SIGNALING PROTEIN / PHOSPHATASE / LIGAND SPECIFICITY / Acetylation / Polymorphism / Centromere / Cytoplasm / Cytoskeleton / Hydrolase / Iron / Manganese / Metal-binding / Methylation / Nucleus / Phosphoprotein / Protein phosphatase / SIGNALING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


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 ...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 / 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 / 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 / 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 / protein heterodimerization activity / neuronal cell body / dendrite / synapse
Similarity search - Function
: / : / 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 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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Chem-XT2 / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement / Resolution: 2.96 Å
AuthorsJeffrey, P.D. / Huhn, J. / Shi, Y.
CitationJournal: Chem.Res.Toxicol. / Year: 2009
Title: A structural basis for the reduced toxicity of dinophysistoxin-2.
Authors: Huhn, J. / Jeffrey, P.D. / Larsen, K. / Rundberget, T. / Rise, F. / Cox, N.R. / Arcus, V. / Shi, Y. / Miles, C.O.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2188
Polymers101,0142
Non-polymers1,2036
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-59 kcal/mol
Surface area35980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.410, 197.240, 201.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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

#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: 65378.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30153
#2: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 35636.152 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 31 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-XT2 / (2R)-2-hydroxy-3-[(2S,5R,6R,8S)-5-hydroxy-8-{(1R,2E)-3-[(2R,4a'R,5R,6'S,8'R,8a'S)-8'-hydroxy-6'-{(1S,3S)-1-hydroxy-3-[( 2S,6R,11S)-11-methyl-1,7-dioxaspiro[5.5]undec-2-yl]butyl}-7'-methylideneoctahydro-3H,3'H-spiro[furan-2,2'-pyrano[3,2-b]p yran]-5-yl]-1-methylprop-2-en-1-yl}-10-methyl-1,7-dioxaspiro[5.5]undec-10-en-2-yl]-2-methylpropanoic acid / DINOPHYSISTOXIN-2


Mass: 805.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H68O13
#5: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.6 Å3/Da / Density % sol: 73.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M LITHIUM SULFATE, 1.5 M AMMONIUM SULFATE, 0.1 M TRIS-CL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Aug 2, 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: 2.95→50 Å / Num. all: 39083 / Num. obs: 39083 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 139.4 Å2 / Rsym value: 0.082
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 4 % / Rsym value: 0.439 / % possible all: 99.9

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Rigid body refinement
Starting model: pdb entry 2IE4

2ie4


Resolution: 2.96→29.81 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2439426.18 / 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
Rfree0.263 1918 4.9 %RANDOM
Rwork0.222 ---
obs0.222 39046 99.5 %-
all-39046 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.8995 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 65.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.17 Å20 Å20 Å2
2---4.76 Å20 Å2
3---10.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.96→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6849 0 74 25 6948
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
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: 2.96→3.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 304 5 %
Rwork0.336 5721 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dtx2.paramdtx2.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5param_mn.inptopo_mn.inp

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