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- PDB-4rh5: Crystal structure of PTPN3 (PTPH1) in complex with Eps15 pTyr849 ... -

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Basic information

Entry
Database: PDB / ID: 4rh5
TitleCrystal structure of PTPN3 (PTPH1) in complex with Eps15 pTyr849 peptide
Components
  • 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 / negative regulation of membrane protein ectodomain proteolysis / ubiquitin-dependent endocytosis / Golgi to endosome transport / clathrin coat of coated pit / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / vesicle organization / clathrin coat assembly ...regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / ubiquitin-dependent endocytosis / Golgi to endosome transport / clathrin coat of coated pit / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / vesicle organization / clathrin coat assembly / regulation of sodium ion transmembrane transport / endocytic recycling / negative regulation of mitotic cell cycle / aggresome / endosomal transport / ciliary membrane / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of receptor recycling / sodium channel regulator activity / polyubiquitin modification-dependent protein binding / cytoskeletal protein binding / receptor-mediated endocytosis of virus by host cell / clathrin-coated pit / phosphotyrosine residue binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / ubiquitin binding / EGFR downregulation / Negative regulation of MET activity / SH3 domain binding / cytoplasmic side of plasma membrane / endocytosis / Negative regulation of MAPK pathway / Cargo recognition for clathrin-mediated endocytosis / MAPK cascade / regulation of cell population proliferation / Clathrin-mediated endocytosis / regulation of protein localization / ATPase binding / early endosome membrane / cytoskeleton / apical plasma membrane / cadherin binding / intracellular membrane-bounded organelle / calcium ion binding / symbiont entry into host cell / glutamatergic synapse / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / EH domain / 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 / EH domain / 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. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / FERM central domain / Protein tyrosine phosphatase superfamily / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein-Tyrosine Phosphatase; Chain A / 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 profile. / Tyrosine-specific protein phosphatases domain / 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: 1.6 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
DepositionOct 1, 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 / database_2 ...citation / 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 / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Epidermal growth factor receptor substrate 15


Theoretical massNumber of molelcules
Total (without water)36,0122
Polymers36,0122
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-12 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.958, 67.500, 69.621
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 Epidermal growth factor receptor substrate 15 / Protein Eps15 / Protein AF-1p


Mass: 1124.005 Da / Num. of mol.: 1 / Fragment: PTYR849 peptide (UNP RESIDUES 846-854) / Source method: obtained synthetically / Details: Synthetic construct / Source: (synth.) Homo sapiens (human) / References: UniProt: P42566
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 21% 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: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 36684 / Num. obs: 36684 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-IceGUIdata 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 2B49

2b49


Resolution: 1.6→24.872 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 18.82 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1830 5 %RANDOM
Rwork0.1738 ---
all0.1752 36684 --
obs0.1752 36624 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→24.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 0 258 2543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122393
X-RAY DIFFRACTIONf_angle_d1.4233268
X-RAY DIFFRACTIONf_dihedral_angle_d13.953908
X-RAY DIFFRACTIONf_chiral_restr0.055369
X-RAY DIFFRACTIONf_plane_restr0.007420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6003-1.64350.26191250.2198266499
1.6435-1.69190.21631280.19832630100
1.6919-1.74650.22481390.19062646100
1.7465-1.80890.23791400.18042637100
1.8089-1.88130.22811530.17432633100
1.8813-1.96690.23151560.17762619100
1.9669-2.07050.23251360.18152668100
2.0705-2.20020.19981330.17532669100
2.2002-2.36990.21211440.17542660100
2.3699-2.60820.2081450.17272695100
2.6082-2.98510.21531350.17972691100
2.9851-3.75880.18661540.16812725100
3.7588-24.87450.16571420.15742857100

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