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- PDB-7jul: Crystal structure of non phosphorylated PTEN (n-crPTEN-13sp-T1, S... -

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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


PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / 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 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 / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / 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 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 / synapse maturation / Regulation of PTEN mRNA translation / Negative regulation of the PI3K/AKT network / cellular response to electrical stimulus / negative regulation of cell cycle G1/S phase transition / negative regulation of axonogenesis / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / myelin sheath adaxonal region / Transcriptional Regulation by MECP2 / negative regulation of organ growth / negative regulation of excitatory postsynaptic potential / forebrain morphogenesis / negative regulation of focal adhesion assembly / phosphatidylinositol dephosphorylation / anaphase-promoting complex binding / Schmidt-Lanterman incisure / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / negative regulation of cyclin-dependent protein serine/threonine kinase activity / dentate gyrus development / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / spindle assembly involved in female meiosis / maternal behavior / positive regulation of ubiquitin-dependent protein catabolic process / phosphatidylinositol biosynthetic process / negative regulation of cell size / dendritic spine morphogenesis / negative regulation of epithelial to mesenchymal transition / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of G1/S transition of mitotic cell cycle / protein serine/threonine phosphatase activity / molecular function inhibitor activity / myosin phosphatase activity / protein-serine/threonine phosphatase / adult behavior / ubiquitin-specific protease binding / regulation of neuron projection development / negative regulation of peptidyl-serine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / locomotor rhythm / negative regulation of cellular senescence / Synthesis of PIPs at the plasma membrane / negative regulation of vascular associated smooth muscle cell proliferation / phosphoprotein phosphatase activity / social behavior / positive regulation of excitatory postsynaptic potential / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / multicellular organismal response to stress / canonical Wnt signaling pathway / prepulse inhibition / synapse assembly / protein dephosphorylation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of PTEN localization / protein-tyrosine-phosphatase / negative regulation of protein phosphorylation / negative regulation of cell migration / protein tyrosine phosphatase activity / cell projection / central nervous system development / cell motility / locomotory behavior / TP53 Regulates Metabolic Genes / PDZ domain binding / 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 / negative regulation of neuron projection development / Downstream TCR signaling / heart development / dendritic spine / postsynaptic density / learning or memory / protein stabilization / Ub-specific processing proteases / neuron projection / apical plasma membrane / negative regulation of cell population proliferation / lipid binding / positive regulation of cell population proliferation
Similarity search - Function
Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / 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 ...Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / 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, 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

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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


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

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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: 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

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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: 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

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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

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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 %

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