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- PDB-7jvx: Crystal structure of PTEN (aa 7-353 followed by spacer TGGGSGGTGG... -

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Basic information

Entry
Database: PDB / ID: 7jvx
TitleCrystal structure of PTEN (aa 7-353 followed by spacer TGGGSGGTGGGSGGTGGGCY ligated to peptide pSDpTpTDpSDPENEPFDED)
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
KeywordsSIGNALING PROTEIN / 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 / Resolution: 3.2 Å
Model detailsCrystal Structure of 4p-PTEN (aa 7-353+ 20 aa spacer, GGGSGGTGGGSGGTGGGCY+CRYpSDpTpTDpSDPENEG
AuthorsDempsey, D. / Phan, K. / Cole, P. / Gabelli, S.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) 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 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)48,7453
Polymers48,5551
Non-polymers1902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.390, 113.390, 57.900
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: 48555.484 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.: 2 / Source method: obtained synthetically / Formula: PO4
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: 1.91 Å3/Da / Density % sol: 35.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 300 mM citrate

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / 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: 2.9→19.8 Å / Num. obs: 7482 / % possible obs: 90.3 % / Redundancy: 2.691 % / Biso Wilson estimate: 68.088 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.212 / Rrim(I) all: 0.252 / Χ2: 0.883 / Net I/σ(I): 3.19 / Num. measured all: 20136 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-3.21.4660.5790.812393208516320.7050.79678.3
3.2-3.51.8240.4181.682163143411860.8450.53182.7
3.5-43.3210.3922.725078154715290.8860.46298.8
4-53.3390.2274.585142155515400.9420.26999
5-63.5310.2055.2124016866800.9480.23899.1
6-103.1950.1365.9123557617370.9860.16196.8
10-19.83.3930.1018.326042181780.9830.11881.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D5R

1d5r


Resolution: 3.2→19.8 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.862 / WRfactor Rfree: 0.2944 / WRfactor Rwork: 0.2509 / FOM work R set: 0.6512 / SU B: 51.656 / SU ML: 0.812 / SU Rfree: 0.6801 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.68 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2965 314 5.4 %RANDOM
Rwork0.2444 ---
obs0.2472 5538 94.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.8 Å2 / Biso mean: 85.335 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--6.3 Å2-0 Å2-0 Å2
2---6.3 Å20 Å2
3---12.6 Å2
Refinement stepCycle: final / Resolution: 3.2→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 10 0 2639
Biso mean--120.53 --
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132711
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172532
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6543656
X-RAY DIFFRACTIONr_angle_other_deg1.4991.5885832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6535312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78921.824159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.91615478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1661518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023028
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02680
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 21 -
Rwork0.388 351 -
all-372 -
obs--82.12 %

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