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- PDB-4qum: Crystal structure of PTPN3 (PTPH1) in complex with a dually phosp... -

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Basic information

Entry
Database: PDB / ID: 4qum
TitleCrystal structure of PTPN3 (PTPH1) in complex with a dually phosphorylated MAPK12 peptide
Components
  • Mitogen-activated protein kinase 12
  • Tyrosine-protein phosphatase non-receptor type 3
KeywordsHYDROLASE / Alpha Beta
Function / homology
Function and homology information


positive regulation of peptidase activity / regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transporter activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / muscle organ development / DSCAM interactions / positive regulation of muscle cell differentiation / Myogenesis ...positive regulation of peptidase activity / regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transporter activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / muscle organ development / DSCAM interactions / positive regulation of muscle cell differentiation / Myogenesis / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of cell cycle / negative regulation of mitotic cell cycle / MAP kinase activity / sodium channel regulator activity / mitogen-activated protein kinase / signal transduction in response to DNA damage / p38MAPK events / cytoskeletal protein binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / liver regeneration / EGFR downregulation / NOD1/2 Signaling Pathway / cytoplasmic side of plasma membrane / VEGFA-VEGFR2 Pathway / Negative regulation of MAPK pathway / MAPK cascade / ATPase binding / peptidyl-serine phosphorylation / cytoskeleton / regulation of cell cycle / intracellular signal transduction / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein kinase 12 / Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / 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 ...Mitogen-activated protein kinase 12 / Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / 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. / Mitogen-activated protein (MAP) kinase p38-like / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / Protein tyrosine phosphatase superfamily / FERM superfamily, second domain / Protein-Tyrosine Phosphatase; Chain A / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 3 / Mitogen-activated protein kinase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.516 Å
AuthorsChen, K.E. / Meng, T.C. / Wang, A.H.J.
CitationJournal: Sci.Signal. / Year: 2014
Title: Reciprocal allosteric regulation of p38 gamma and PTPN3 involves a PDZ domain-modulated complex formation.
Authors: Chen, K.E. / Lin, S.Y. / Wu, M.J. / Ho, M.R. / Santhanam, A. / Chou, C.C. / Meng, T.C. / Wang, A.H.J.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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: Mitogen-activated protein kinase 12


Theoretical massNumber of molelcules
Total (without water)36,1322
Polymers36,1322
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-16 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.491, 75.491, 109.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P26045, protein-tyrosine-phosphatase
#2: Protein/peptide Mitogen-activated protein kinase 12 / MAP kinase 12 / MAPK 12 / Extracellular signal-regulated kinase 6 / ERK-6 / Mitogen-activated ...MAP kinase 12 / MAPK 12 / Extracellular signal-regulated kinase 6 / ERK-6 / Mitogen-activated protein kinase p38 gamma / MAP kinase p38 gamma / Stress-activated protein kinase 3


Mass: 1244.252 Da / Num. of mol.: 1 / Fragment: Activation loop (UNP RESIDUES 182-190) / Mutation: W190R / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P53778, mitogen-activated protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 30% PEG 8000, 5% glycerol, 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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 6, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. all: 12505 / Num. obs: 12505 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 10.79
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 4 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.35 / Num. unique all: 1182 / % possible all: 95.1

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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: 2.516→31.325 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 25.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 611 4.9 %RANDOM
Rwork0.197 ---
all0.1993 12505 --
obs0.1993 12481 98.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.516→31.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 0 27 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092364
X-RAY DIFFRACTIONf_angle_d1.2523221
X-RAY DIFFRACTIONf_dihedral_angle_d15.435881
X-RAY DIFFRACTIONf_chiral_restr0.046366
X-RAY DIFFRACTIONf_plane_restr0.005411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5155-2.76860.33021700.247288198
2.7686-3.16880.27251540.22712982100
3.1688-3.99110.24851420.18953011100
3.9911-31.32750.20861450.177299695

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