[English] 日本語
Yorodumi
- PDB-5bzx: Crystal structure of human phosphatase PTEN treated with a bisper... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bzx
TitleCrystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
KeywordsHYDROLASE / phosphatase / C2 domain / disulfide / oxidized / vanadate
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 / negative regulation of peptidyl-serine phosphorylation / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity ...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 / negative regulation of peptidyl-serine phosphorylation / 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 / Negative regulation of the PI3K/AKT network / synapse maturation / negative regulation of cell cycle G1/S phase transition / Regulation of PTEN mRNA translation / myelin sheath adaxonal region / cellular response to electrical stimulus / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / presynaptic membrane assembly / negative regulation of axonogenesis / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / Transcriptional Regulation by MECP2 / negative regulation of organ growth / forebrain morphogenesis / negative regulation of focal adhesion assembly / phosphatidylinositol dephosphorylation / negative regulation of excitatory postsynaptic potential / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / anaphase-promoting complex binding / Schmidt-Lanterman incisure / dentate gyrus development / ubiquitin ligase activator activity / phosphatidylinositol biosynthetic process / dendritic spine morphogenesis / maternal behavior / spindle assembly involved in female meiosis / negative regulation of cell size / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of epithelial to mesenchymal transition / molecular function inhibitor activity / protein-serine/threonine phosphatase / negative regulation of G1/S transition of mitotic cell cycle / regulation of neuron projection development / ubiquitin-specific protease binding / protein serine/threonine phosphatase activity / Synthesis of IP3 and IP4 in the cytosol / locomotor rhythm / Synthesis of PIPs at the plasma membrane / adult behavior / positive regulation of intracellular signal transduction / negative regulation of vascular associated smooth muscle cell proliferation / phosphoprotein phosphatase activity / negative regulation of cellular senescence / social behavior / positive regulation of excitatory postsynaptic potential / negative regulation of osteoblast differentiation / multicellular organismal response to stress / prepulse inhibition / protein dephosphorylation / synapse assembly / protein-tyrosine-phosphatase / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tyrosine phosphatase activity / Regulation of PTEN localization / negative regulation of cell migration / central nervous system development / cell projection / PDZ domain binding / TP53 Regulates Metabolic Genes / locomotory behavior / cell motility / phosphatidylinositol 3-kinase/protein kinase B signal transduction / beta-catenin binding / PML body / regulation of protein stability / 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 / heart development / dendritic spine / learning or memory / neuron projection / Ub-specific processing proteases / protein stabilization / postsynaptic density / apical plasma membrane / negative regulation of cell population proliferation / apoptotic process / positive regulation of cell population proliferation / lipid binding / enzyme binding / positive regulation of transcription by RNA polymerase II
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 / VANADATE ION / 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: 2.5 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 11, 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 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)149,9119
Polymers149,2314
Non-polymers6805
Water15,853880
1
A: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4232
Polymers37,3081
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
3
C: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5733
Polymers37,3081
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)207.060, 206.900, 87.670
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
11A-510-

HOH

21A-522-

HOH

31A-624-

HOH

41C-620-

HOH

-
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 7-353 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-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


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


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.9 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.77119 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: 1.77119 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11K, H, -L20.499
ReflectionResolution: 2.5→46.293 Å / Num. obs: 65393 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.91 % / Biso Wilson estimate: 56.698 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.123 / Χ2: 0.949 / Net I/σ(I): 17.43 / Num. measured all: 843899
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
2.5-2.60.7311.5521.5387652714771451.619100
2.6-2.70.8511.12.2577080614461421.147100
2.7-2.80.9210.8193.0467403534153410.854100
2.8-2.90.960.5764.3458498459145900.6100
2.9-30.9780.4245.7149248404940490.442100
3-3.10.980.3796.5642575349734960.396100
3.1-40.9980.1318.5124842618312183110.135100
4-60.9990.05539.8614957111341113410.057100
6-80.9990.05139.7335011283328320.054100
8-1010.03457.6913692102410240.036100
10-1510.03565.55107157787780.036100
15-2010.03959.4324761921920.041100
2010.03552.5115521671520.03791

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7 Å46.29 Å
Translation7 Å46.29 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1d5r
Resolution: 2.5→46.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1852 / WRfactor Rwork: 0.1601 / FOM work R set: 0.8448 / SU B: 4.673 / SU ML: 0.111 / SU R Cruickshank DPI: 0.0763 / SU Rfree: 0.0467 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 3297 5 %RANDOM
Rwork0.1752 ---
obs0.1767 62095 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.99 Å2 / Biso mean: 59.842 Å2 / Biso min: 29.37 Å2
Baniso -1Baniso -2Baniso -3
1--33.11 Å20 Å20 Å2
2---30.39 Å20 Å2
3---63.5 Å2
Refinement stepCycle: final / Resolution: 2.5→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10310 0 40 880 11230
Biso mean--55.13 57.52 -
Num. residues----1256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910650
X-RAY DIFFRACTIONr_bond_other_d0.0060.029820
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.95214409
X-RAY DIFFRACTIONr_angle_other_deg1.451322568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.4651252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76223.499543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.237151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5341562
X-RAY DIFFRACTIONr_chiral_restr0.0880.21488
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112052
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022672
X-RAY DIFFRACTIONr_mcbond_it3.556.1095020
X-RAY DIFFRACTIONr_mcbond_other3.5496.1085019
X-RAY DIFFRACTIONr_mcangle_it5.6669.1636268
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 231 -
Rwork0.342 4369 -
all-4600 -
obs--96.27 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more