+Open data
-Basic information
Entry | Database: PDB / ID: 8fna | ||||||
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Title | Crystal structure of the C-terminal Fg domain of human TNR | ||||||
Components | Tenascin-R | ||||||
Keywords | SIGNALING PROTEIN / Extracellular matrix / Fibrinogen | ||||||
Function / homology | Function and homology information axon extension involved in regeneration / negative regulation of axon extension involved in regeneration / perineuronal net / tenascin complex / positive regulation of transmission of nerve impulse / neuroblast migration / telencephalon cell migration / neuron cell-cell adhesion / negative regulation of synaptic transmission / negative regulation of cell-cell adhesion ...axon extension involved in regeneration / negative regulation of axon extension involved in regeneration / perineuronal net / tenascin complex / positive regulation of transmission of nerve impulse / neuroblast migration / telencephalon cell migration / neuron cell-cell adhesion / negative regulation of synaptic transmission / negative regulation of cell-cell adhesion / regulation of cell differentiation / locomotory exploration behavior / associative learning / neuromuscular process controlling balance / ECM proteoglycans / regulation of cell adhesion / regulation of cell migration / extracellular matrix organization / positive regulation of synaptic transmission, glutamatergic / axon guidance / synaptic transmission, glutamatergic / long-term synaptic potentiation / synapse organization / Schaffer collateral - CA1 synapse / negative regulation of neuron projection development / collagen-containing extracellular matrix / cell adhesion / membrane raft / glutamatergic synapse / cell surface / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 8fna.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fna.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 8fna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fna_validation.pdf.gz | 964.1 KB | Display | wwPDB validaton report |
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Full document | 8fna_full_validation.pdf.gz | 965.6 KB | Display | |
Data in XML | 8fna_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 8fna_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/8fna ftp://data.pdbj.org/pub/pdb/validation_reports/fn/8fna | HTTPS FTP |
-Related structure data
Related structure data | 8fn8C 8fn9C 8fnbC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27219.246 Da / Num. of mol.: 1 / Fragment: Fg domain (UNP residues 1129-1358) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNR / Production host: Escherichia coli (E. coli) / References: UniProt: Q92752 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% PEG3350, 0.2 M L-proline, 100 mM HEPES sodium, pH 7.5, 5 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 27862 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.17 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.06 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2576 / CC1/2: 0.845 / Rpim(I) all: 0.24 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2J3F Resolution: 1.75→38.08 Å / SU ML: 0.1424 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.4322 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: 29.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→38.08 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 / Auth asym-ID: A / Label asym-ID: A
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