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Yorodumi- PDB-6mti: Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) in... -
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-Basic information
Entry | Database: PDB / ID: 6mti | ||||||
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Title | Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+ | ||||||
Components |
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Keywords | EXOCYTOSIS / SNARE / lipid nanotubes | ||||||
Function / homology | Function and homology information trans-Golgi Network Vesicle Budding / BLOC-1 complex / 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 / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling ...trans-Golgi Network Vesicle Budding / BLOC-1 complex / 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 / 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 / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / spontaneous neurotransmitter secretion / Lysosome Vesicle Biogenesis / 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 / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / regulation of synaptic vesicle priming / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulated exocytosis / calcium ion sensor activity / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / regulation of establishment of protein localization / storage vacuole / regulation of calcium ion-dependent exocytosis / 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 / 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 / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / regulation of exocytosis / Clathrin-mediated endocytosis / 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 / positive regulation of hormone secretion / neurotransmitter secretion / neurotransmitter receptor internalization / calcium-dependent phospholipid binding / ATP-dependent protein binding / protein localization to membrane / neuron projection terminus / presynaptic cytosol / regulation of synaptic vesicle recycling / neurotransmitter transport / insulin secretion / syntaxin binding / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / clathrin-coated vesicle / Neutrophil degranulation / synaptic vesicle priming / endosomal transport / regulation of synaptic vesicle exocytosis / regulation of synapse assembly / postsynaptic cytosol / low-density lipoprotein particle receptor binding / clathrin binding / myosin binding / regulation of dopamine secretion / regulation of neuron projection development / phosphatidylserine binding / exocytosis / voltage-gated potassium channel activity / positive regulation of exocytosis / presynaptic active zone / synaptic vesicle exocytosis / modulation of excitatory postsynaptic potential Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10.4 Å | ||||||
Authors | Grushin, K. / Wang, J. / Coleman, J. / Rothman, J. / Sindelar, C. / Krishnakumar, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis for the clamping and Ca activation of SNARE-mediated fusion by synaptotagmin. Authors: Kirill Grushin / Jing Wang / Jeff Coleman / James E Rothman / Charles V Sindelar / Shyam S Krishnakumar / Abstract: Synapotagmin-1 (Syt1) interacts with both SNARE proteins and lipid membranes to synchronize neurotransmitter release to calcium (Ca) influx. Here we report the cryo-electron microscopy structure of ...Synapotagmin-1 (Syt1) interacts with both SNARE proteins and lipid membranes to synchronize neurotransmitter release to calcium (Ca) influx. Here we report the cryo-electron microscopy structure of the Syt1-SNARE complex on anionic-lipid containing membranes. Under resting conditions, the Syt1 C2 domains bind the membrane with a magnesium (Mg)-mediated partial insertion of the aliphatic loops, alongside weak interactions with the anionic lipid headgroups. The C2B domain concurrently interacts the SNARE bundle via the 'primary' interface and is positioned between the SNAREpins and the membrane. In this configuration, Syt1 is projected to sterically delay the complete assembly of the associated SNAREpins and thus, contribute to clamping fusion. This Syt1-SNARE organization is disrupted upon Ca-influx as Syt1 reorients into the membrane, likely displacing the attached SNAREpins and reversing the fusion clamp. We thus conclude that the cation (Mg/Ca) dependent membrane interaction is a key determinant of the dual clamp/activator function of Synaptotagmin-1. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6mti.cif.gz | 574.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mti.ent.gz | 473.8 KB | Display | PDB format |
PDBx/mmJSON format | 6mti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mti_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6mti_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6mti_validation.xml.gz | 96.2 KB | Display | |
Data in CIF | 6mti_validation.cif.gz | 136.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/6mti ftp://data.pdbj.org/pub/pdb/validation_reports/mt/6mti | HTTPS FTP |
-Related structure data
Related structure data | 9231MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Synaptotagmin- ... , 2 types, 6 molecules 162345
#1: Protein | Mass: 14654.769 Da / Num. of mol.: 2 / Fragment: C2A domain, residues 141-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21707 #2: Protein | Mass: 32247.197 Da / Num. of mol.: 4 / Fragment: C2A and C2B domains, residues 141-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21707 |
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-Protein , 2 types, 12 molecules AEIMQUBFJNRV
#3: Protein | Mass: 7231.061 Da / Num. of mol.: 6 / Fragment: residues 28-89 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2, Syb2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63045 #4: Protein | Mass: 7837.957 Da / Num. of mol.: 6 / Fragment: residues 191-256 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851 |
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-Synaptosomal-associated protein ... , 2 types, 12 molecules CGKOSWDHLPTX
#5: Protein | Mass: 9030.114 Da / Num. of mol.: 6 / Fragment: residues 7-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881 #6: Protein | Mass: 7471.368 Da / Num. of mol.: 6 / Fragment: residues 141-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881 |
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-Non-polymers , 1 types, 10 molecules
#7: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Synaptotagmin-1 C2A and C2B domains in the complex with SNARE proteins on the surface of lipid membrane nanotube Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: Situs / Category: model fitting |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Helical symmerty | Angular rotation/subunit: 78.48 ° / Axial rise/subunit: 7.3 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2082 / Symmetry type: HELICAL |
Atomic model building | Protocol: RIGID BODY FIT |
Atomic model building | PDB-ID: 5CCI Accession code: 5CCI / Source name: PDB / Type: experimental model |