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- PDB-5bug: Crystal structure of human phosphatase PTEN oxidized by H2O2 -

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Basic information

Entry
Database: PDB / ID: 5bug
TitleCrystal structure of human phosphatase PTEN oxidized by H2O2
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
KeywordsHYDROLASE / C2 domain / disulfide / oxidized
Function / homology
Function and homology information


PTEN Loss of Function in Cancer / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance ...PTEN Loss of Function in Cancer / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / phosphatidylinositol-3-phosphate phosphatase activity / central nervous system neuron axonogenesis / postsynaptic density assembly / neuron-neuron synaptic transmission / presynaptic membrane assembly / Regulation of PTEN mRNA translation / synapse maturation / Negative regulation of the PI3K/AKT network / negative regulation of cell cycle G1/S phase transition / cellular response to electrical stimulus / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of axonogenesis / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / Transcriptional Regulation by MECP2 / myelin sheath adaxonal region / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of organ growth / negative regulation of excitatory postsynaptic potential / forebrain morphogenesis / negative regulation of focal adhesion assembly / phosphatidylinositol dephosphorylation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / anaphase-promoting complex binding / Schmidt-Lanterman incisure / dentate gyrus development / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / phosphatidylinositol biosynthetic process / dendritic spine morphogenesis / negative regulation of cell size / maternal behavior / spindle assembly involved in female meiosis / negative regulation of peptidyl-serine phosphorylation / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of epithelial to mesenchymal transition / molecular function inhibitor activity / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / negative regulation of G1/S transition of mitotic cell cycle / regulation of neuron projection development / ubiquitin-specific protease binding / Synthesis of IP3 and IP4 in the cytosol / social behavior / locomotor rhythm / adult behavior / negative regulation of vascular associated smooth muscle cell proliferation / Synthesis of PIPs at the plasma membrane / positive regulation of intracellular signal transduction / phosphoprotein phosphatase activity / negative regulation of cellular senescence / positive regulation of excitatory postsynaptic potential / negative regulation of osteoblast differentiation / prepulse inhibition / multicellular organismal response to stress / synapse assembly / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of PTEN localization / negative regulation of cell migration / central nervous system development / cell projection / PDZ domain binding / TP53 Regulates Metabolic Genes / locomotory behavior / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell motility / regulation of protein stability / beta-catenin binding / PML body / cytoplasmic side of plasma membrane / Regulation of PTEN stability and activity / Ovarian tumor domain proteases / Downstream TCR signaling / cell migration / negative regulation of neuron projection development
Similarity search - Function
Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / Immunoglobulin-like - #1110 / Inositol hexakisphosphate / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. ...Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / Immunoglobulin-like - #1110 / Inositol hexakisphosphate / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Polymorphic toxin system, DSP-PTPase phosphatase / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsLee, C.-U. / Bier, D. / Hennig, S. / Grossmann, T.N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGR3592/2-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Redox Modulation of PTEN Phosphatase Activity by Hydrogen Peroxide and Bisperoxidovanadium Complexes.
Authors: Lee, C.U. / Hahne, G. / Hanske, J. / Bange, T. / Bier, D. / Rademacher, C. / Hennig, S. / Grossmann, T.N.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
B: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
C: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
D: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,8328
Polymers149,2314
Non-polymers6004
Water13,529751
1
A: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4582
Polymers37,3081
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4582
Polymers37,3081
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4582
Polymers37,3081
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4582
Polymers37,3081
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.870, 206.830, 87.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-660-

HOH

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Components

#1: Protein
Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / Mutated in multiple advanced cancers 1 / Phosphatase and tensin homolog


Mass: 37307.805 Da / Num. of mol.: 4 / Fragment: PTEN wt 14-351 delta 286-309 / Mutation: Deletion 286-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTEN, MMAC1, TEP1 / Plasmid: pFH1
Details (production host): Bacmid DNA derived from pFH1 transformed in DH10Bac E. coli
Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P60484, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase
#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Fragment: L-tartrate / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11K, H, -L20.5
ReflectionHighest resolution: 2.4 Å / Num. obs: 73497 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 57.846 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.104 / Χ2: 0.961 / Net I/σ(I): 19.82 / Num. measured all: 881196
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.50.7761.5851.5995199834883471.66100
2.5-2.60.8631.1732.1885407712071191.225100
2.6-2.70.9180.8233.1876859612861260.858100
2.7-2.80.9620.6164.1866226532753270.643100
2.8-2.90.9770.4315.8656363457045700.45100
2.9-30.9880.3167.8649418404340430.33100
3-3.10.9880.2749.1641674347734770.286100
3.1-40.9990.09324.1922067118233182320.097100
4-610.04149.9813314711294112930.043100
6-80.9990.03950.7633239282428240.041100
8-1010.02764.7710471101810170.02999.9
10-1510.02975.9591547777770.03100
15-200.9990.03369.721101921920.035100
2010.03458.2812581671530.03891.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7 Å48.76 Å
Translation7 Å48.76 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1d5r

1d5r


Resolution: 2.4→48.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1913 / WRfactor Rwork: 0.1612 / FOM work R set: 0.845 / SU B: 4.186 / SU ML: 0.102 / SU R Cruickshank DPI: 0.06 / SU Rfree: 0.0435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 3663 5 %RANDOM
Rwork0.1752 ---
obs0.1769 69833 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.18 Å2 / Biso mean: 62.403 Å2 / Biso min: 29.14 Å2
Baniso -1Baniso -2Baniso -3
1--32.28 Å20 Å20 Å2
2---31.41 Å20 Å2
3---63.69 Å2
Refinement stepCycle: final / Resolution: 2.4→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10338 0 40 751 11129
Biso mean--80.83 57.49 -
Num. residues----1256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910682
X-RAY DIFFRACTIONr_bond_other_d0.0070.029847
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.95214449
X-RAY DIFFRACTIONr_angle_other_deg1.458322648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.39751252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67423.601547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.754151785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3651559
X-RAY DIFFRACTIONr_chiral_restr0.0970.21488
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112085
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022674
X-RAY DIFFRACTIONr_mcbond_it3.8486.3135020
X-RAY DIFFRACTIONr_mcbond_other3.8496.3125019
X-RAY DIFFRACTIONr_mcangle_it6.1619.4666268
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 264 -
Rwork0.309 5034 -
all-5298 -
obs--99.29 %

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