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Yorodumi- PDB-2ed8: Solution structure of the second fibronectin type III domain of h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ed8 | ||||||
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Title | Solution structure of the second fibronectin type III domain of human Netrin receptor DCC | ||||||
Components | Netrin receptor DCC | ||||||
Keywords | APOPTOSIS / Tumor suppressor protein DCC / Colorectal cancer suppressor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / negative regulation of collateral sprouting / Role of second messengers in netrin-1 signaling / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of dendrite development / Netrin mediated repulsion signals / Caspase activation via Dependence Receptors in the absence of ligand ...dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / negative regulation of collateral sprouting / Role of second messengers in netrin-1 signaling / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of dendrite development / Netrin mediated repulsion signals / Caspase activation via Dependence Receptors in the absence of ligand / DCC mediated attractive signaling / DSCAM interactions / postsynaptic modulation of chemical synaptic transmission / axonal growth cone / axonogenesis / axon guidance / postsynaptic density membrane / neuron migration / Schaffer collateral - CA1 synapse / cell-cell adhesion / transmembrane signaling receptor activity / negative regulation of neuron projection development / apoptotic process / cell surface / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Tochio, N. / Koshiba, S. / Tomizawa, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the second fibronectin type III domain of human Netrin receptor DCC Authors: Tochio, N. / Koshiba, S. / Tomizawa, T. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ed8.cif.gz | 603.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ed8.ent.gz | 504.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ed8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/2ed8 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/2ed8 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11204.281 Da / Num. of mol.: 1 / Fragment: second fn3 domain, Fibronectin type-III 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: DCC / Plasmid: P050905-21 / References: UniProt: P43146 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.2mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |