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- PDB-2n1t: Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution -
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Basic information
Entry | Database: PDB / ID: 2n1t | ||||||
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Title | Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution | ||||||
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![]() | EXOCYTOSIS / Synaptotagmin-1 / C2B domain / Syntaxin-1A / Synaptobrevin-2 / SNAP-25 / SNAP-25A / SNARE complex | ||||||
Function / homology | ![]() Toxicity of botulinum toxin type C (botC) / clathrin-sculpted acetylcholine transport vesicle membrane / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / trans-Golgi Network Vesicle Budding / clathrin-sculpted glutamate transport vesicle membrane / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter ...Toxicity of botulinum toxin type C (botC) / clathrin-sculpted acetylcholine transport vesicle membrane / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / trans-Golgi Network Vesicle Budding / clathrin-sculpted glutamate transport vesicle membrane / regulation of delayed rectifier potassium channel activity / 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 / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / extrinsic component of presynaptic membrane / Acetylcholine Neurotransmitter Release Cycle / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / Toxicity of botulinum toxin type A (botA) / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / Lysosome Vesicle Biogenesis / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / zymogen granule membrane / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / regulation of synaptic vesicle priming / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulated exocytosis / calcium ion sensor activity / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / storage vacuole / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / eosinophil degranulation / vesicle docking / exocytic vesicle / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / regulation of exocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / positive regulation of dendrite extension / Golgi to plasma membrane protein transport / neurotransmitter secretion / neurotransmitter receptor internalization / calcium-dependent phospholipid binding / ATP-dependent protein binding / protein localization to membrane / neuron projection terminus / regulation of synaptic vesicle recycling / Neurexins and neuroligins / neurotransmitter transport / Sensory processing of sound by inner hair cells of the cochlea / insulin secretion / syntaxin binding / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / clathrin-coated vesicle / synaptic vesicle priming / endosomal transport / regulation of synapse assembly / postsynaptic cytosol / Other interleukin signaling / low-density lipoprotein particle receptor binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 712.2 KB | Display | ![]() |
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PDB format | ![]() | 599.2 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
#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.) ![]() ![]() ![]() |
#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.) ![]() ![]() ![]() |
#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.) ![]() ![]() ![]() |
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 |