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Yorodumi- PDB-5ttt: Sparse-restraint solution NMR structure of micelle-solubilized cy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ttt | ||||||
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Title | Sparse-restraint solution NMR structure of micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4 refined by restrained Rosetta | ||||||
Components | Degenerin mec-4 | ||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information negative regulation of turning behavior involved in mating / positive regulation of detection of mechanical stimulus involved in sensory perception of touch / positive regulation of mechanosensory behavior / Sensory perception of salty taste / Stimuli-sensing channels / neuron projection membrane / detection of mechanical stimulus involved in sensory perception of touch / ligand-gated sodium channel activity / mechanosensory behavior / sodium ion transmembrane transport ...negative regulation of turning behavior involved in mating / positive regulation of detection of mechanical stimulus involved in sensory perception of touch / positive regulation of mechanosensory behavior / Sensory perception of salty taste / Stimuli-sensing channels / neuron projection membrane / detection of mechanical stimulus involved in sensory perception of touch / ligand-gated sodium channel activity / mechanosensory behavior / sodium ion transmembrane transport / response to mechanical stimulus / potassium ion transport / axon / membrane Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Everett, J.K. / Liu, G. / Mao, B. / Driscoll, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Sparse-restraint solution NMR structure of micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4 refined by restrained Rosetta Authors: Everett, J.K. / Liu, G. / Mao, B. / Driscoll, M.A. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ttt.cif.gz | 688.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ttt.ent.gz | 578.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ttt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/5ttt ftp://data.pdbj.org/pub/pdb/validation_reports/tt/5ttt | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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Details | Monomer as determined by light scatering |
-Components
#1: Protein | Mass: 13296.793 Da / Num. of mol.: 1 / Fragment: residues 1-103 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mec-4, mec-13, T01C8.7 / Production host: Escherichia coli (E. coli) / References: UniProt: P24612 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1.5 mM [U-13C; U-15N; U-2H] micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4, 95% H2O/5% D2O Details: 1.5 MM [U-100% 13C; U-100% 15N; 100% 2H; ILV METHYL 1H; FY RING 1H] MEC4, 25 MM SODIUM; PHOSPHATE, 5 MM ZWITTERGENT 3-12, 25 MM SODIUM CHLORIDE, 5MM TCEP, 95% H2O/5% D2O Label: CND / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 1.5 mM Component: micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4 Isotopic labeling: [U-13C; U-15N; U-2H] |
Sample conditions | Details: 1.5 MM [U-100% 13C; U-100% 15N; 100% 2H; ILV METHYL 1H; FY RING 1H] MEC4, 25 MM SODIUM; PHOSPHATE, 5 MM ZWITTERGENT 3-12, 25 MM SODIUM CHLORIDE, 5MM TCEP, 95% H2O/5% D2O Ionic strength: 0.025 M / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 300 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: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 250 / Conformers submitted total number: 20 |