[English] 日本語
Yorodumi
- PDB-7jul: Crystal structure of non phosphorylated PTEN (n-crPTEN-13sp-T1, S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jul
TitleCrystal structure of non phosphorylated PTEN (n-crPTEN-13sp-T1, SDTTDSDPENEG)
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
KeywordsTRANSFERASE / HYDROLASE / phosphatase / Phosphatidylinositol 3 / 4 / 5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
Function / homology
Function and homology information


inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance ...inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / 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 / cellular response to electrical stimulus / negative regulation of cell cycle G1/S phase transition / Transcriptional Regulation by MECP2 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of axonogenesis / myelin sheath adaxonal region / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / negative regulation of excitatory postsynaptic potential / negative regulation of organ growth / forebrain morphogenesis / negative regulation of focal adhesion assembly / Schmidt-Lanterman incisure / anaphase-promoting complex binding / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatidylinositol dephosphorylation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / dentate gyrus development / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / maternal behavior / positive regulation of ubiquitin-dependent protein catabolic process / spindle assembly involved in female meiosis / phosphatidylinositol biosynthetic process / negative regulation of cell size / dendritic spine morphogenesis / negative regulation of epithelial to mesenchymal transition / negative regulation of vascular associated smooth muscle cell proliferation / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / protein serine/threonine phosphatase activity / adult behavior / molecular function inhibitor activity / protein-serine/threonine phosphatase / ubiquitin-specific protease binding / regulation of neuron projection development / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-serine phosphorylation / locomotor rhythm / negative regulation of cellular senescence / Synthesis of PIPs at the plasma membrane / phosphoprotein phosphatase activity / positive regulation of excitatory postsynaptic potential / social behavior / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / multicellular organismal response to stress / prepulse inhibition / synapse assembly / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of PTEN localization / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of protein phosphorylation / negative regulation of cell migration / protein tyrosine phosphatase activity / central nervous system development / locomotory behavior / cell projection / PDZ domain binding / cell motility / TP53 Regulates Metabolic Genes / positive regulation of DNA-binding transcription factor activity / regulation of protein stability / PML body / cytoplasmic side of plasma membrane / Regulation of PTEN stability and activity / Ovarian tumor domain proteases / cell migration / Downstream TCR signaling / negative regulation of neuron projection development / heart development / learning or memory / dendritic spine / postsynaptic density / protein stabilization / Ub-specific processing proteases / neuron projection / apical plasma membrane / negative regulation of cell population proliferation / positive regulation of cell population proliferation / lipid binding
Similarity search - Function
PTEN, phosphatase domain / Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / : / 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 ...PTEN, phosphatase domain / Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / : / 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 / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / 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
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.53 Å
AuthorsDempsey, D. / Phan, K. / Cole, P. / Gabelli, S.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA74305 United States
Department of Defense (DOD, United States) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM130961 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2021
Title: The structural basis of PTEN regulation by multi-site phosphorylation.
Authors: Dempsey, D.R. / Viennet, T. / Iwase, R. / Park, E. / Henriquez, S. / Chen, Z. / Jeliazkov, J.R. / Palanski, B.A. / Phan, K.L. / Coote, P. / Gray, J.J. / Eck, M.J. / Gabelli, S.B. / Arthanari, H. / Cole, P.A.
History
DepositionAug 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 2.0Feb 2, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / entity_name_com / entity_src_gen / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _citation.title / _entity.pdbx_description ..._citation.title / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _pdbx_contact_author.id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs
Description: Model orientation/position
Details: We uploaded an older pdb of the initial refinements;
Provider: author / Type: Coordinate replacement
Revision 2.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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


Theoretical massNumber of molelcules
Total (without water)40,8861
Polymers40,8861
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.123, 113.123, 57.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

-
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: 40886.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTEN, MMAC1, TEP1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P60484, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 1:1 volume of well solution: 100 mM Bis-Tris propane pH 7.0, 1.2 M DL-malic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.53→28.81 Å / Num. obs: 12325 / % possible obs: 99.7 % / Redundancy: 8.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.028 / Rrim(I) all: 0.081 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.53-2.646.90.5611027914790.9090.2220.6052.697.9
8.75-28.798.20.0425873160.9990.0140.04336.797.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1D5R

1d5r


Resolution: 2.53→28.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2359 / WRfactor Rwork: 0.1821 / FOM work R set: 0.7964 / SU B: 11.863 / SU ML: 0.249 / SU R Cruickshank DPI: 0.7323 / SU Rfree: 0.2863 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.732 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 605 4.9 %RANDOM
Rwork0.1836 ---
obs0.1861 11720 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 181.37 Å2 / Biso mean: 68.482 Å2 / Biso min: 28.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 2.53→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 0 10 2652
Biso mean---46.76 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132716
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172495
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.6553660
X-RAY DIFFRACTIONr_angle_other_deg1.2161.5845793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2255313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21221.824159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04515485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3671518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
LS refinement shellResolution: 2.53→2.592 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.454 43 -
Rwork0.343 841 -
obs--96.51 %

+
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://pdbjlvh1.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