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Yorodumi- PDB-2n1t: Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n1t | ||||||
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Title | Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution | ||||||
Components |
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Keywords | EXOCYTOSIS / Synaptotagmin-1 / C2B domain / Syntaxin-1A / Synaptobrevin-2 / SNAP-25 / SNAP-25A / SNARE complex | ||||||
Function / homology | Function and homology information Toxicity of botulinum toxin type C (botC) / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / Toxicity of botulinum toxin type E (botE) / myosin head/neck binding / synchronous neurotransmitter secretion ...Toxicity of botulinum toxin type C (botC) / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / Toxicity of botulinum toxin type E (botE) / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Toxicity of botulinum toxin type A (botA) / Other interleukin signaling / calcium-dependent activation of synaptic vesicle fusion / Acetylcholine Neurotransmitter Release Cycle / regulation of regulated secretory pathway / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / calcium ion sensor activity / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / clathrin-sculpted monoamine transport vesicle membrane / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / Lysosome Vesicle Biogenesis / positive regulation of norepinephrine secretion / regulation of synaptic vesicle priming / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / zymogen granule membrane / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / chromaffin granule membrane / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / ribbon synapse / storage vacuole / synaptic vesicle docking / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Dopamine Neurotransmitter Release Cycle / eosinophil degranulation / Norepinephrine Neurotransmitter Release Cycle / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / chloride channel inhibitor activity / SNARE complex / Golgi to plasma membrane protein transport / SNAP receptor activity / positive regulation of dopamine secretion / protein heterooligomerization / secretion by cell / regulation of vesicle-mediated transport / Glutamate Neurotransmitter Release Cycle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / regulation of exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / neurotransmitter receptor internalization / calcium-dependent phospholipid binding / ATP-dependent protein binding / neurotransmitter transport / neuron projection terminus / protein localization to membrane / regulation of synaptic vesicle recycling / Neurexins and neuroligins / Sensory processing of sound by inner hair cells of the cochlea / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / insulin secretion / synaptic vesicle priming / syntaxin binding / clathrin-coated vesicle / regulation of synapse assembly / endosomal transport / low-density lipoprotein particle receptor binding / clathrin binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Brewer, K. / Bacaj, T. / Cavalli, A. / Camilloni, C. / Swarbrick, J. / Liu, J. / Zhou, A. / Zhou, P. / Barlow, N. / Xu, J. ...Brewer, K. / Bacaj, T. / Cavalli, A. / Camilloni, C. / Swarbrick, J. / Liu, J. / Zhou, A. / Zhou, P. / Barlow, N. / Xu, J. / Seven, A. / Prinslow, E. / Voleti, R. / Haussinger, D. / Bonvin, A. / Tomchick, D. / Vendruscolo, M. / Graham, B. / Sudhof, T. / Rizo, J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 Title: Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution. Authors: Brewer, K.D. / Bacaj, T. / Cavalli, A. / Camilloni, C. / Swarbrick, J.D. / Liu, J. / Zhou, A. / Zhou, P. / Barlow, N. / Xu, J. / Seven, A.B. / Prinslow, E.A. / Voleti, R. / Haussinger, D. / ...Authors: Brewer, K.D. / Bacaj, T. / Cavalli, A. / Camilloni, C. / Swarbrick, J.D. / Liu, J. / Zhou, A. / Zhou, P. / Barlow, N. / Xu, J. / Seven, A.B. / Prinslow, E.A. / Voleti, R. / Haussinger, D. / Bonvin, A.M. / Tomchick, D.R. / Vendruscolo, M. / Graham, B. / 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 | 2n1t.cif.gz | 712.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n1t.ent.gz | 599.2 KB | Display | PDB format |
PDBx/mmJSON format | 2n1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/2n1t ftp://data.pdbj.org/pub/pdb/validation_reports/n1/2n1t | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
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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-Components
#1: Protein | Mass: 8045.023 Da / Num. of mol.: 1 / Fragment: UNP residues 25-93 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syb2, Vamp2 / Plasmid: pGEX-KT / Production host: Escherichia coli (E. coli) / References: UniProt: P63045 |
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#2: Protein | Mass: 8429.528 Da / Num. of mol.: 1 / Fragment: UNP residues 188-259 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sap, Stx1a / Plasmid: pGEX-KT / Production host: Escherichia coli (E. coli) / References: UniProt: P32851 |
#3: Protein | Mass: 9030.114 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 7-83) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP, SNAP25, SNAP-25A / Plasmid: pGEX-KT / Production host: Escherichia coli (E. coli) / References: UniProt: P60880 |
#4: Protein | Mass: 8458.420 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 131-204) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP, SNAP25, SNAP-25A / Plasmid: pGEX-KT / Production host: Escherichia coli (E. coli) / References: UniProt: P60880 |
#5: Protein | Mass: 17465.236 Da / Num. of mol.: 1 / Fragment: C2B domain (UNP residues 272-419) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SVP65, SYT, SYT1 / Plasmid: pGEX-KT / Production host: Escherichia coli (E. coli) / References: UniProt: P21579 |
Compound details | RESIDUE ASP 41 OF SNAP-25 N-TERMINAL DOMAIN (CHAIN C) WAS MUTATED TO CYS, AND LABELED WITH DY-C2 ...RESIDUE ASP 41 OF SNAP-25 N-TERMINAL DOMAIN (CHAIN C) WAS MUTATED TO CYS, AND LABELED WITH DY-C2 TAG IN SOME SAMPLES. |
Sequence details | THE SEQUENCES OF CHAIN C AND D MATCH ISOFORM 2 SEQUENCE WITH UNIPROT IDENTIFIER |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: This deposition includes five conformers of the synaptotagmin-1 C2B domain SNARE complex. This complex is highly dynamic under the solution conditions used in the measurement of ...Details: This deposition includes five conformers of the synaptotagmin-1 C2B domain SNARE complex. This complex is highly dynamic under the solution conditions used in the measurement of pseudocontact shifts by NMR spectroscopy that provided the structural information for this analysis. Because of this highly dynamic nature, no single structure can be considered as 'the structure' of this complex under our conditions. The five conformers deposited must be considered as just a few of the many conformers that form the ensemble but illustrate the types of interactions between the synaptotagmin-1 C2B domain and the SNARE complex that mediate this dynamic binding mode. | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 30 uM [U-100% 13C; U-100% 15N] protein, 25 mM Tris-HCl, 125 mM KSCN, 1 mM CaCl2, 90% H2O/10% D2O Label: sample_1 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | pH: 7.4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 3 Details: MOLECULAR DYNAMICS SIMULATIONS WERE USED TO GENERATE STRUCTURES OF THE SYNAPTOTAGMIN-1 C2B DOMAIN-SNARE COMPLEX THAT COULD BE EVALUATED BASED ON HOW WELL THEY FIT THE MEASURED PSEUDOCONTACT ...Details: MOLECULAR DYNAMICS SIMULATIONS WERE USED TO GENERATE STRUCTURES OF THE SYNAPTOTAGMIN-1 C2B DOMAIN-SNARE COMPLEX THAT COULD BE EVALUATED BASED ON HOW WELL THEY FIT THE MEASURED PSEUDOCONTACT SHIFTS. SINCE IT WAS CLEAR FROM THE ANALYSIS THAT THE COMPLEX IS HIGHLY DYNAMICS AND NO SINGLE STRUCTURE CAN FIT ALL THE DATA, THE STRUCTURES FROM THE SIMULATIONS WERE USED TO TRY TO FIT THE MEASURED PSEUDOCONTACT SHIFTS AS ENSEMBLED-AVERAGED VALUES. THE STRUCTURES IN THE DEPOSITION ARE AMONG THOSE THAT CONTRIBUTED TO THE BEST ENSEMBLE-AVERAGE FITS. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: all these conformers contribute to this dynamics ensemble | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Contribution to fit PCS data / Conformers calculated total number: 10000 / Conformers submitted total number: 5 |