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- PDB-8cqy: Crystal structure of the PTPN3 PDZ domain bound to the PBM TACE C... -

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Basic information

Entry
Database: PDB / ID: 8cqy
TitleCrystal structure of the PTPN3 PDZ domain bound to the PBM TACE C-terminal peptide
Components
  • Disintegrin and metalloproteinase domain-containing protein 17
  • Tyrosine-protein phosphatase non-receptor type 3
KeywordsHYDROLASE / protein tyrosine phosphatase PTPN3 / PDZ domains / PDZ-binding motif
Function / homology
Function and homology information


regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transport / negative regulation of mitotic cell cycle / negative regulation of epidermal growth factor receptor signaling pathway / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transport / negative regulation of mitotic cell cycle / negative regulation of epidermal growth factor receptor signaling pathway / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / EGFR downregulation / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / MAPK cascade / ATPase binding / cytoskeleton / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / Domain of unknown function DUF3850 / Domain of unknown function (DUF3850) / ASCH / ASCH 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 / Domain of unknown function DUF3850 / Domain of unknown function (DUF3850) / ASCH / ASCH 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 / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PUA-like superfamily / FERM central domain / FERM superfamily, second domain / 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 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 3 / DUF3850 domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGenera, M. / Colcombet-Cazenave, B. / Croitoru, A. / Raynal, B. / Mechaly, A. / Caillet, J. / Haouz, A. / Wolff, N. / Caillet-Saguy, C.
Funding support France, 2items
OrganizationGrant numberCountry
Pasteur Institute France
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Front Mol Biosci / Year: 2023
Title: Interactions of the protein tyrosine phosphatase PTPN3 with viral and cellular partners through its PDZ domain: insights into structural determinants and phosphatase activity.
Authors: Genera, M. / Colcombet-Cazenave, B. / Croitoru, A. / Raynal, B. / Mechaly, A. / Caillet, J. / Haouz, A. / Wolff, N. / Caillet-Saguy, C.
History
DepositionMar 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 3
B: Disintegrin and metalloproteinase domain-containing protein 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2234
Polymers14,1772
Non-polymers462
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-16 kcal/mol
Surface area5890 Å2
Unit cell
Length a, b, c (Å)76.878, 76.878, 46.253
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-102-

HOH

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Components

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


Mass: 12709.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN3, PTPH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26045, protein-tyrosine-phosphatase
#2: Protein/peptide Disintegrin and metalloproteinase domain-containing protein 17 / ADAM 17 / Snake venom-like protease / TNF-alpha convertase / TNF-alpha-converting enzyme


Mass: 1467.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78536, EC: 3.4.24.86
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 3350, 0.2 M NaSCN at pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→66.58 Å / Num. obs: 17566 / % possible obs: 99.5 % / Redundancy: 13.9 % / CC1/2: 0.997 / Net I/σ(I): 12.51
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 1726 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→66.58 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.258 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20258 903 5.1 %RANDOM
Rwork0.16756 ---
obs0.1694 16687 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.01 Å2
Baniso -1Baniso -2Baniso -3
1-15.09 Å20 Å20 Å2
2--15.09 Å20 Å2
3----30.18 Å2
Refinement stepCycle: 1 / Resolution: 1.7→66.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 2 22 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.014793
X-RAY DIFFRACTIONr_bond_other_d0.0010.017730
X-RAY DIFFRACTIONr_angle_refined_deg2.6481.6651066
X-RAY DIFFRACTIONr_angle_other_deg1.1571.6421722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.964596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60121.52246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56315151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.199158
X-RAY DIFFRACTIONr_chiral_restr0.1580.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02880
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02124
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0073.455393
X-RAY DIFFRACTIONr_mcbond_other4.0033.457392
X-RAY DIFFRACTIONr_mcangle_it5.5625.142486
X-RAY DIFFRACTIONr_mcangle_other5.5575.14487
X-RAY DIFFRACTIONr_scbond_it5.2734.077400
X-RAY DIFFRACTIONr_scbond_other5.2554.079399
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4085.863580
X-RAY DIFFRACTIONr_long_range_B_refined9.95742.296808
X-RAY DIFFRACTIONr_long_range_B_other9.96142.298806
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.599 61 -
Rwork0.831 1209 -
obs--98.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10060.24-0.14240.6414-0.45321.1903-0.0178-0.00260.0054-0.0320.03630.00860.0246-0.0549-0.01850.1033-0.0041-0.0010.04920.00240.002339.1652-10.2883-2.074
21.39940.87090.75780.9105-0.53283.16460.07910.00590.04580.0934-0.03350.0583-0.13130.1252-0.04560.1474-0.0077-0.01040.04050.00290.006841.7231.4698-0.6299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 97
2X-RAY DIFFRACTION2B1 - 6

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