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Yorodumi- PDB-1byn: SOLUTION STRUCTURE OF THE CALCIUM-BOUND FIRST C2-DOMAIN OF SYNAPT... -
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-Basic information
Entry | Database: PDB / ID: 1byn | ||||||
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Title | SOLUTION STRUCTURE OF THE CALCIUM-BOUND FIRST C2-DOMAIN OF SYNAPTOTAGMIN I | ||||||
Components | PROTEIN (SYNAPTOTAGMIN I) | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / SYNAPTOTAGMIN / C2-DOMAIN / EXOCYTOSIS / NEUROTRANSMITTER RELEASE / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle ...synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / calcium-ion regulated exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / regulation of synaptic vesicle exocytosis / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle exocytosis / excitatory synapse / synaptic vesicle endocytosis / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / SNARE binding / secretory granule / phospholipid binding / terminal bouton / synaptic vesicle membrane / response to calcium ion / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Shao, X. / Fernandez, I. / Sudhof, T.C. / Rizo, J. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Solution structures of the Ca2+-free and Ca2+-bound C2A domain of synaptotagmin I: does Ca2+ induce a conformational change? Authors: Shao, X. / Fernandez, I. / Sudhof, T.C. / Rizo, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1byn.cif.gz | 811.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1byn.ent.gz | 703.2 KB | Display | PDB format |
PDBx/mmJSON format | 1byn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1byn ftp://data.pdbj.org/pub/pdb/validation_reports/by/1byn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14783.882 Da / Num. of mol.: 1 / Fragment: C2A-DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P21707 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | Ionic strength: 100 mM NACL / pH: 5.0 / Temperature: 307 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian UNITY 500 / Manufacturer: Varian / Model: UNITY 500 / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR ensemble | Conformer selection criteria: FEWEST RESTRAINTS VIOLATIONS / Conformers calculated total number: 100 / Conformers submitted total number: 20 |