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Yorodumi- PDB-3d42: Crystal structure of HePTP in complex with a monophosphorylated E... -
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-Basic information
Entry | Database: PDB / ID: 3d42 | ||||||
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Title | Crystal structure of HePTP in complex with a monophosphorylated Erk2 peptide | ||||||
Components |
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Keywords | HYDROLASE / HEPTP / HUMAN HEMATOPOIETIC TYROSINE PHOSPHATASE CATALYTIC DOMAIN MUTANT / LC-PTP / PTPN7 / ERK2 / PTP-PEPTIDE COMPLEX / MAPK-DERIVED PEPTIDE / Phosphoprotein / Protein phosphatase / ATP-binding / Cell cycle / Host-virus interaction / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Transferase | ||||||
Function / homology | Function and homology information phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / ERKs are inactivated / cytosine metabolic process ...phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / ERKs are inactivated / cytosine metabolic process / response to epidermal growth factor / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / Interleukin-37 signaling / positive regulation of macrophage proliferation / Regulation of the apoptosome activity / outer ear morphogenesis / regulation of cellular pH / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / progesterone receptor signaling pathway / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / pseudopodium / Recycling pathway of L1 / MAPK1 (ERK2) activation / Bergmann glial cell differentiation / negative regulation of cell differentiation / positive regulation of telomere capping / thyroid gland development / Advanced glycosylation endproduct receptor signaling / non-membrane spanning protein tyrosine phosphatase activity / steroid hormone receptor signaling pathway / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate NADPH Oxidases / Regulation of HSF1-mediated heat shock response / MAP kinase activity / regulation of ossification / RHO GTPases Activate WASPs and WAVEs / phosphatase binding / mitogen-activated protein kinase / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / Schwann cell development / Growth hormone receptor signaling / stress-activated MAPK cascade / lipopolysaccharide-mediated signaling pathway / : / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / NPAS4 regulates expression of target genes / ERK1 and ERK2 cascade / myelination / cellular response to amino acid starvation / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / protein dephosphorylation / RNA polymerase II CTD heptapeptide repeat kinase activity / ESR-mediated signaling / protein-tyrosine-phosphatase / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / protein tyrosine phosphatase activity / Signal transduction by L1 / caveola / long-term synaptic potentiation / Negative regulation of FGFR3 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / FCERI mediated MAPK activation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / FCGR3A-mediated phagocytosis / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / peptidyl-threonine phosphorylation / B cell receptor signaling pathway / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / response to nicotine Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Critton, D.A. / Tortajada, A. / Page, R. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural basis of substrate recognition by hematopoietic tyrosine phosphatase. Authors: Critton, D.A. / Tortajada, A. / Stetson, G. / Peti, W. / Page, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d42.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d42.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 3d42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d42_validation.pdf.gz | 467.6 KB | Display | wwPDB validaton report |
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Full document | 3d42_full_validation.pdf.gz | 471.6 KB | Display | |
Data in XML | 3d42_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3d42_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/3d42 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/3d42 | HTTPS FTP |
-Related structure data
Related structure data | 2hvlC 2qdcC 3d44C 2qdmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35202.711 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP residues 65-360) / Mutation: T106D, C270S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN7 / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P35236, protein-tyrosine-phosphatase |
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#2: Protein/peptide | Mass: 1033.050 Da / Num. of mol.: 1 / Fragment: Activation loop (UNP residues 184-191) / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS / References: UniProt: P28482 |
#3: Chemical | ChemComp-TAR / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.2 M AMMONIUM TARTRATE DIBASIC, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 29, 2008 Details: SI(III) CHANNEL CUT MONOCHROMATOR, OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI(III) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 11129 / Num. obs: 10896 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.111 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.221 / Num. unique all: 1048 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QDM Resolution: 2.46→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.88 / SU B: 7.943 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.813 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.455→2.518 Å / Total num. of bins used: 20
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