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- PDB-7juk: Crystal structure of PTEN with a tetra-phosphorylated tail (4p-cr... -

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Basic information

Entry
Database: PDB / ID: 7juk
TitleCrystal structure of PTEN with a tetra-phosphorylated tail (4p-crPTEN-13sp-T2, SDTTDSDPENEG)
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
KeywordsSIGNALING PROTEIN / 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 / 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 / forebrain morphogenesis / negative regulation of excitatory postsynaptic potential / 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 / PML body / beta-catenin binding / 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 / : / 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
PHOSPHATE 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: 3.15 Å
Model detailsCrystal Structure of 4p-PTEN (aa 7-353+ 13 aa spacer, TGGGSGGTGGCRY+pSDpTpTDpSDPENEG
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)
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM130961 United States
Department of Defense (DOD, United States) 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 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 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 1.2Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9812
Polymers40,8861
Non-polymers951
Water181
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)113.444, 113.444, 57.005
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 / Plasmid: pfastbac / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.2 M DL-malic acid

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.15→80.217 Å / Num. all: 6346 / Num. obs: 6346 / % possible obs: 99.3 % / Redundancy: 6.6 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.152 / Rsym value: 0.14 / Net I/av σ(I): 3.3 / Net I/σ(I): 8.8 / Num. measured all: 41598
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.15-3.326.30.7151.155028780.3060.7790.7152.795.9
3.32-3.526.30.4751.654758740.2080.5190.4753.8100
3.52-3.766.70.3132.455058190.1320.340.3135.8100
3.76-4.076.40.2283.249937760.0980.2490.2287.5100
4.07-4.456.90.1574.148697010.0650.170.15710.4100
4.45-4.986.90.1145.245036510.0470.1240.11413.499.9
4.98-5.756.70.1125.737865660.0470.1210.11212.7100
5.75-7.046.30.1085.331024910.0470.1180.10812.7100
7.04-9.966.50.0885.524393770.0380.0960.08816.399.9
9.96-28.5036.70.086614242130.0350.0930.08619.796.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.39
Highest resolutionLowest resolution
Rotation28.5 Å3.5 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
MOLREPphasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D5R

1d5r


Resolution: 3.15→28.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.859 / WRfactor Rfree: 0.2907 / WRfactor Rwork: 0.183 / FOM work R set: 0.7737 / SU B: 28.893 / SU ML: 0.487 / SU Rfree: 0.6127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.613 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 322 5.1 %RANDOM
Rwork0.1836 ---
obs0.1887 6023 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 219.49 Å2 / Biso mean: 90.408 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--3.77 Å20 Å20 Å2
2---3.77 Å20 Å2
3---7.54 Å2
Refinement stepCycle: final / Resolution: 3.15→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 5 1 2631
Biso mean--30 30 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132699
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172473
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.6553639
X-RAY DIFFRACTIONr_angle_other_deg1.1291.5835741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4575311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03421.824159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98915478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6931518
X-RAY DIFFRACTIONr_chiral_restr0.0580.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02623
LS refinement shellResolution: 3.15→3.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 11 -
Rwork0.3 397 -
all-408 -
obs--91.69 %

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