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- PDB-4s0g: Crystal structure of PTPN3 (PTPH1) in complex with Eps15 pTyr849 ... -

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Basic information

Entry
Database: PDB / ID: 4s0g
TitleCrystal structure of PTPN3 (PTPH1) in complex with Eps15 pTyr849 P850V peptide
Components
  • Peptide from Epidermal growth factor receptor substrate 15
  • Tyrosine-protein phosphatase non-receptor type 3
KeywordsHYDROLASE/PROTEIN BINDING / Alpha Beta / Hydrolase / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


regulation of membrane depolarization during action potential / regulation of sodium ion transmembrane transporter activity / negative regulation of membrane protein ectodomain proteolysis / Golgi to endosome transport / clathrin coat of coated pit / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / endocytic recycling / aggresome ...regulation of membrane depolarization during action potential / regulation of sodium ion transmembrane transporter activity / negative regulation of membrane protein ectodomain proteolysis / Golgi to endosome transport / clathrin coat of coated pit / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / endocytic recycling / aggresome / endosomal transport / positive regulation of receptor recycling / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / polyubiquitin modification-dependent protein binding / sodium channel regulator activity / clathrin-coated pit / cytoskeletal protein binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / protein tyrosine phosphatase activity / liver regeneration / EGFR downregulation / Negative regulation of MET activity / SH3 domain binding / cytoplasmic side of plasma membrane / endocytosis / Negative regulation of MAPK pathway / MAPK cascade / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / regulation of cell population proliferation / ATPase binding / early endosome membrane / postsynapse / receptor-mediated endocytosis of virus by host cell / cytoskeleton / cadherin binding / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal ...Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / Ubiquitin-interacting motif. / FERM domain signature 2. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Protein tyrosine phosphatase superfamily / FERM central domain / FERM superfamily, second domain / Protein-Tyrosine Phosphatase; Chain A / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 3 / Epidermal growth factor receptor substrate 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.723 Å
AuthorsChen, K.-E. / Meng, T.C. / Wang, A.H.-J.
CitationJournal: Structure / Year: 2015
Title: Substrate specificity and plasticity of FERM-containing protein tyrosine phosphatases.
Authors: Chen, K.E. / Li, M.Y. / Chou, C.C. / Ho, M.R. / Chen, G.C. / Meng, T.C. / Wang, A.H.
History
DepositionDec 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 3
B: Peptide from Epidermal growth factor receptor substrate 15


Theoretical massNumber of molelcules
Total (without water)36,0142
Polymers36,0142
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-12 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.051, 67.332, 68.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 3 / Protein-tyrosine phosphatase H1 / PTP-H1


Mass: 34887.664 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 628-909 / Mutation: D811A, C842S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPH1, PTPN3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P26045, protein-tyrosine-phosphatase
#2: Protein/peptide Peptide from Epidermal growth factor receptor substrate 15 / Protein Eps15 / Protein AF-1p


Mass: 1126.021 Da / Num. of mol.: 1 / Fragment: Phosphotyrosine 849 peptide, UNP residues 846-854 / Mutation: P850V / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42566
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.87 Å3/Da / Density % sol: 34.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 26% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 2, 2014
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. all: 28900 / Num. obs: 28900 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2839 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BSSdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4RH5

4rh5


Resolution: 1.723→37.076 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 23.02 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1461 5.06 %RANDOM
Rwork0.1823 ---
obs0.1845 28863 98.76 %-
all-28900 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.723→37.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 0 137 2415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122359
X-RAY DIFFRACTIONf_angle_d1.3093217
X-RAY DIFFRACTIONf_dihedral_angle_d14.686883
X-RAY DIFFRACTIONf_chiral_restr0.057365
X-RAY DIFFRACTIONf_plane_restr0.006412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7232-1.78480.33481510.2974262396
1.7848-1.85630.30851480.26082711100
1.8563-1.94070.25721330.2239273199
1.9407-2.04310.25031720.21142703100
2.0431-2.1710.25031510.18892744100
2.171-2.33870.22931440.18252744100
2.3387-2.57390.23041420.1877275299
2.5739-2.94630.24151530.1849275799
2.9463-3.71140.21431260.16652836100
3.7114-37.0850.18111410.148280195

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