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- PDB-1d5r: Crystal Structure of the PTEN Tumor Suppressor -

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Basic information

Entry
Database: PDB / ID: 1d5r
TitleCrystal Structure of the PTEN Tumor Suppressor
ComponentsPHOSPHOINOSITIDE PHOSPHATASE PTEN
KeywordsHYDROLASE / C2 DOMAIN / PHOSPHOTIDYLINOSITOL / PHOSPHATASE
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 / regulation of cellular component size / 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 ...inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / 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 / negative regulation of dendritic spine morphogenesis / 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 / negative regulation of axonogenesis / Transcriptional Regulation by MECP2 / 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 / negative regulation of epithelial to mesenchymal transition / phosphatidylinositol dephosphorylation / anaphase-promoting complex binding / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / dentate gyrus development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / positive regulation of ubiquitin-dependent protein catabolic process / spindle assembly involved in female meiosis / phosphatidylinositol biosynthetic process / dendritic spine morphogenesis / negative regulation of cell size / brain morphogenesis / myosin phosphatase activity / protein serine/threonine phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / molecular function inhibitor activity / ubiquitin-specific protease binding / protein-serine/threonine phosphatase / regulation of neuron projection development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of IP3 and IP4 in the cytosol / locomotor rhythm / negative regulation of cellular senescence / negative regulation of vascular associated smooth muscle cell proliferation / social behavior / phosphoprotein phosphatase activity / positive regulation of excitatory postsynaptic potential / Synthesis of PIPs at the plasma membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / multicellular organismal response to stress / localization / prepulse inhibition / negative regulation of peptidyl-serine phosphorylation / synapse assembly / Regulation of PTEN localization / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of cell migration / negative regulation of protein phosphorylation / locomotory behavior / phosphatidylinositol 3-kinase/protein kinase B signal transduction / central nervous system development / protein tyrosine phosphatase activity / cell projection / cell motility / PDZ domain binding / TP53 Regulates Metabolic Genes / regulation of protein stability / cytoplasmic side of plasma membrane / PML body / Regulation of PTEN stability and activity / positive regulation of DNA-binding transcription factor activity / cell migration / Ovarian tumor domain proteases / 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
Similarity search - Function
PTEN, phosphatase domain / Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / Inositol hexakisphosphate / Immunoglobulin-like - #1110 / 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 / Immunoglobulin-like - #1110 / 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 superfamily / Protein-Tyrosine Phosphatase; Chain A / 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. / C2 domain superfamily / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsLee, J.O. / Yang, H. / Georgescu, M.-M. / Di Cristofano, A. / Pavletich, N.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association.
Authors: Lee, J.O. / Yang, H. / Georgescu, M.M. / Di Cristofano, A. / Maehama, T. / Shi, Y. / Dixon, J.E. / Pandolfi, P. / Pavletich, N.P.
History
DepositionOct 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 24, 2016Group: Structure summary
Revision 1.4Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOINOSITIDE PHOSPHATASE PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6462
Polymers38,4961
Non-polymers1501
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.140, 113.140, 58.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein PHOSPHOINOSITIDE PHOSPHATASE PTEN


Mass: 38496.184 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-353 / Mutation: RESIDUES 286-309 ARE REPLACED BY VAL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PVL1393 / Cell line (production host): HIGH FIVE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60484, protein-tyrosine-phosphatase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 286-309 ARE REPLACED BY VAL

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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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: NA/K TARTRATE, 5% GLYCEROL, 100MM TRIS-CL, 10MM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 MNa/K L(+)-tartrate1reservoir
25-10 %(v/v)glycerol1reservoir
3100 mMTris-Cl1reservoir
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 20548 / Num. obs: 20302 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 42.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.163 / % possible all: 76.4
Reflection
*PLUS
Num. measured all: 188143

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.276 960 -RANDOM
Rwork0.224 ---
all0.226 20548 --
obs0.226 20302 95.8 %-
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 10 382 2968
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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