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- PDB-4ny3: Human PTPA in complex with peptide -

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Basic information

Entry
Database: PDB / ID: 4ny3
TitleHuman PTPA in complex with peptide
Components
  • Serine/threonine-protein phosphatase 2A activator
  • Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
KeywordsHYDROLASE ACTIVATOR / PTPA / PPP2R4 / REGULATORY SUBUNIT B' (PR 53) / PROTEIN PHOSPHATASE 2A (PP2A)
Function / homology
Function and homology information


protein tyrosine phosphatase activator activity / negative regulation of protein dephosphorylation / Integration of energy metabolism / regulation of phosphoprotein phosphatase activity / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation ...protein tyrosine phosphatase activator activity / negative regulation of protein dephosphorylation / Integration of energy metabolism / regulation of phosphoprotein phosphatase activity / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / positive regulation of microtubule binding / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / protein phosphatase regulator activity / GABA receptor binding / negative regulation of epithelial to mesenchymal transition / 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 / 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 / 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 / protein serine/threonine phosphatase activity / negative regulation of phosphoprotein phosphatase activity / CTLA4 inhibitory signaling / ATPase complex / Platelet sensitization by LDL / protein-serine/threonine phosphatase / regulation of cell differentiation / T cell homeostasis / ERK/MAPK targets / regulation of G1/S transition of mitotic cell cycle / phosphoprotein phosphatase activity / mesoderm development / positive regulation of phosphoprotein phosphatase activity / chromosome, centromeric region / DARPP-32 events / 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 / positive regulation of protein dephosphorylation / Resolution of Sister Chromatid Cohesion / calcium channel complex / protein dephosphorylation / mitotic spindle organization / meiotic cell cycle / protein phosphatase 2A binding / peptidylprolyl isomerase / protein tyrosine phosphatase activity / peptidyl-prolyl cis-trans isomerase activity / RHO GTPases Activate Formins / response to lead ion / regulation of protein phosphorylation / Spry regulation of FGF signaling / RAF activation / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / tau protein binding / positive regulation of protein serine/threonine kinase activity / spindle pole / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Cyclin D associated events in G1 / microtubule cytoskeleton / Regulation of TP53 Degradation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / intracellular signal transduction / positive regulation of apoptotic process / membrane raft / protein heterodimerization activity / signaling receptor binding / synapse / protein homodimerization activity / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphotyrosyl phosphate activator, C-terminal lid domain / Phosphotyrosyl phosphatase activator, PTPA / PTPA superfamily / Phosphotyrosyl phosphatase activator, C-terminal lid domain / Phosphotyrosyl phosphate activator (PTPA) protein / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type ...Phosphotyrosyl phosphate activator, C-terminal lid domain / Phosphotyrosyl phosphatase activator, PTPA / PTPA superfamily / Phosphotyrosyl phosphatase activator, C-terminal lid domain / Phosphotyrosyl phosphate activator (PTPA) protein / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Serine/threonine-protein phosphatase 2A activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsLoew, C. / Quistgaard, E.M. / Nordlund, P.
CitationJournal: Biol.Chem. / Year: 2014
Title: Structural basis for PTPA interaction with the invariant C-terminal tail of PP2A.
Authors: Low, C. / Quistgaard, E.M. / Kovermann, M. / Anandapadamanaban, M. / Balbach, J. / Nordlund, P.
History
DepositionDec 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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 activator
B: Serine/threonine-protein phosphatase 2A activator
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
D: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,55118
Polymers71,2224
Non-polymers1,32914
Water12,665703
1
A: Serine/threonine-protein phosphatase 2A activator
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1838
Polymers35,6112
Non-polymers5726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-59 kcal/mol
Surface area14220 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase 2A activator
D: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,36810
Polymers35,6112
Non-polymers7578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-57 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.670, 47.970, 87.180
Angle α, β, γ (deg.)84.41, 80.23, 88.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serine/threonine-protein phosphatase 2A activator / PP2A / subunit B' / PR53 isoform / Phosphotyrosyl phosphatase activator / PTPA / Serine/threonine- ...PP2A / subunit B' / PR53 isoform / Phosphotyrosyl phosphatase activator / PTPA / Serine/threonine-protein phosphatase 2A regulatory subunit 4 / Serine/threonine-protein phosphatase 2A regulatory subunit B'


Mass: 34856.094 Da / Num. of mol.: 2 / Fragment: UNP Residues 22-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R4, PTPA / Production host: Escherichia coli (E. coli) / References: UniProt: Q15257, peptidylprolyl isomerase
#2: Protein/peptide Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 754.827 Da / Num. of mol.: 2 / Fragment: UNP Residues 304-309 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P67775
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHAINS A,B CORRESPONDS TO ISOFORM 2 OF THE UNP ENTRY Q15257.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M (NH4)2SO4 and 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9687 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2011
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 1.8→29.2 Å / Num. all: 62666 / Num. obs: 62666 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.15
Reflection shellResolution: 1.8→1.84 Å / Rsym value: 0.665 / % possible all: 86.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.797→29.174 Å / SU ML: 0.16 / σ(F): 2 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 1903 3.04 %Random
Rwork0.1582 ---
obs0.159 62666 97 %-
all-62666 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.797→29.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 74 703 5713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035194
X-RAY DIFFRACTIONf_angle_d0.8517062
X-RAY DIFFRACTIONf_dihedral_angle_d12.391910
X-RAY DIFFRACTIONf_chiral_restr0.065759
X-RAY DIFFRACTIONf_plane_restr0.005885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7974-1.84230.24871190.21463877X-RAY DIFFRACTION86
1.8423-1.89210.20371390.18634337X-RAY DIFFRACTION97
1.8921-1.94780.25271200.17864317X-RAY DIFFRACTION97
1.9478-2.01060.19061210.17344361X-RAY DIFFRACTION97
2.0106-2.08250.23191260.16574402X-RAY DIFFRACTION97
2.0825-2.16580.19421310.15874344X-RAY DIFFRACTION97
2.1658-2.26440.19931450.15744356X-RAY DIFFRACTION98
2.2644-2.38370.20571450.15884342X-RAY DIFFRACTION98
2.3837-2.5330.20231250.16174423X-RAY DIFFRACTION98
2.533-2.72840.19361490.1634404X-RAY DIFFRACTION98
2.7284-3.00270.181550.15574359X-RAY DIFFRACTION98
3.0027-3.43660.18711530.15034401X-RAY DIFFRACTION99
3.4366-4.32750.14931330.13514422X-RAY DIFFRACTION99
4.3275-29.17760.15251420.15854418X-RAY DIFFRACTION99

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