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Yorodumi- PDB-8fn9: Crystal structure of the C-terminal Fg domain of TNR with the sin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fn9 | ||||||
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Title | Crystal structure of the C-terminal Fg domain of TNR with the single FN domain of PTPRZ | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex / receptor protein tyrosine phosphatase / extracellular matrix / fibronectin type III / fibrinogen | ||||||
Function / homology | Function and homology information axon extension involved in regeneration / negative regulation of axon extension involved in regeneration / perineuronal net / regulation of oligodendrocyte progenitor proliferation / tenascin complex / positive regulation of transmission of nerve impulse / neuroblast migration / telencephalon cell migration / MDK and PTN in ALK signaling / transmembrane receptor protein tyrosine phosphatase activity ...axon extension involved in regeneration / negative regulation of axon extension involved in regeneration / perineuronal net / regulation of oligodendrocyte progenitor proliferation / tenascin complex / positive regulation of transmission of nerve impulse / neuroblast migration / telencephalon cell migration / MDK and PTN in ALK signaling / transmembrane receptor protein tyrosine phosphatase activity / neuron cell-cell adhesion / negative regulation of synaptic transmission / regulation of myelination / Other interleukin signaling / positive regulation of oligodendrocyte differentiation / negative regulation of cell-cell adhesion / regulation of cell differentiation / oligodendrocyte differentiation / locomotory exploration behavior / associative learning / neuromuscular process controlling balance / peptidyl-tyrosine dephosphorylation / ECM proteoglycans / regulation of cell adhesion / hematopoietic progenitor cell differentiation / regulation of cell migration / protein dephosphorylation / protein-tyrosine-phosphatase / extracellular matrix organization / positive regulation of synaptic transmission, glutamatergic / axonogenesis / protein tyrosine phosphatase activity / synaptic transmission, glutamatergic / central nervous system development / axon guidance / long-term synaptic potentiation / synapse organization / Schaffer collateral - CA1 synapse / integrin binding / negative regulation of neuron projection development / collagen-containing extracellular matrix / negative regulation of neuron apoptotic process / learning or memory / cell adhesion / membrane raft / glutamatergic synapse / synapse / cell surface / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bouyain, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Protein-protein interactions between tenascin-R and RPTP zeta /phosphacan are critical to maintain the architecture of perineuronal nets. Authors: Sinha, A. / Kawakami, J. / Cole, K.S. / Ladutska, A. / Nguyen, M.Y. / Zalmai, M.S. / Holder, B.L. / Broerman, V.M. / Matthews, R.T. / Bouyain, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fn9.cif.gz | 605.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fn9.ent.gz | 443.5 KB | Display | PDB format |
PDBx/mmJSON format | 8fn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fn9_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8fn9_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8fn9_validation.xml.gz | 49.4 KB | Display | |
Data in CIF | 8fn9_validation.cif.gz | 71.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/8fn9 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/8fn9 | HTTPS FTP |
-Related structure data
Related structure data | 8fn8C 8fnaC 8fnbC 1fnaS 2j3fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 27223.234 Da / Num. of mol.: 4 / Fragment: Fg domain (UNP residues 1129-1358) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNR / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92752 #2: Protein | Mass: 11918.245 Da / Num. of mol.: 4 / Fragment: UNP residues 310-411 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRZ1, HTPZP2, PTPRZ, PTPRZ2, PTPZ / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: P23471, protein-tyrosine-phosphatase #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG2000 MME, 200 mM potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 102222 / % possible obs: 91.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.062 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10193 / CC1/2: 0.486 / Rpim(I) all: 0.517 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2J3F & 1FNA Resolution: 1.8→42.96 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.0225 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.96 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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