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- PDB-6mti: Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) in... -

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Basic information

Entry
Database: PDB / ID: 6mti
TitleSynaptotagmin-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
  • (Synaptosomal-associated protein ...) x 2
  • (Synaptotagmin- ...) x 2
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsEXOCYTOSIS / SNARE / lipid nanotubes
Function / homology
Function and homology information


exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of vesicle fusion / regulation of delayed rectifier potassium channel activity / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion ...exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of vesicle fusion / regulation of delayed rectifier potassium channel activity / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / BLOC-1 complex / calcium-dependent activation of synaptic vesicle fusion / myosin head/neck binding / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / Lysosome Vesicle Biogenesis / zymogen granule membrane / storage vacuole / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / calcium ion sensor activity / Norepinephrine Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / eosinophil degranulation / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming / regulated exocytosis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / vesicle-mediated transport in synapse / positive regulation of intracellular protein transport / exocytic vesicle / regulation of establishment of protein localization / positive regulation of calcium ion-dependent exocytosis / vesicle organization / protein heterooligomerization / ribbon synapse / positive regulation of dendrite extension / vesicle docking / regulation of vesicle-mediated transport / regulation of exocytosis / Cargo recognition for clathrin-mediated endocytosis / secretion by cell / chloride channel inhibitor activity / Clathrin-mediated endocytosis / positive regulation of dopamine secretion / SNARE complex / SNAP receptor activity / calcium-ion regulated exocytosis / vesicle fusion / actomyosin / hormone secretion / LGI-ADAM interactions / dense core granule / calcium-dependent phospholipid binding / positive regulation of hormone secretion / neuron projection terminus / membraneless organelle assembly / Golgi to plasma membrane protein transport / ATP-dependent protein binding / neurotransmitter secretion / protein localization to membrane / clathrin-coated vesicle / syntaxin binding / presynaptic active zone / syntaxin-1 binding / regulation of synaptic vesicle recycling / insulin secretion / endosomal transport / Neutrophil degranulation / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / regulation of synapse assembly / SNARE complex assembly / positive regulation of neurotransmitter secretion / neurotransmitter transport / myosin binding / response to gravity / regulation of neuron projection development / synaptic vesicle priming / regulation of synaptic vesicle exocytosis / exocytosis / regulation of dopamine secretion / modulation of excitatory postsynaptic potential / associative learning / protein sumoylation
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptotagmin / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. ...Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptotagmin / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Synaptotagmin-1 / Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10.4 Å
AuthorsGrushin, K. / Wang, J. / Coleman, J. / Rothman, J. / Sindelar, C. / Krishnakumar, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK027044 United States
CitationJournal: 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
DepositionOct 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
1: Synaptotagmin-1
2: Synaptotagmin-1
3: Synaptotagmin-1
4: Synaptotagmin-1
5: Synaptotagmin-1
6: Synaptotagmin-1
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Vesicle-associated membrane protein 2
F: Syntaxin-1A
G: Synaptosomal-associated protein 25
H: Synaptosomal-associated protein 25
I: Vesicle-associated membrane protein 2
J: Syntaxin-1A
K: Synaptosomal-associated protein 25
L: Synaptosomal-associated protein 25
M: Vesicle-associated membrane protein 2
N: Syntaxin-1A
O: Synaptosomal-associated protein 25
P: Synaptosomal-associated protein 25
Q: Vesicle-associated membrane protein 2
R: Syntaxin-1A
S: Synaptosomal-associated protein 25
T: Synaptosomal-associated protein 25
U: Vesicle-associated membrane protein 2
V: Syntaxin-1A
W: Synaptosomal-associated protein 25
X: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,96440
Polymers347,72130
Non-polymers24310
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area88630 Å2
ΔGint-735 kcal/mol
Surface area145330 Å2

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Components

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Synaptotagmin- ... , 2 types, 6 molecules 162345

#1: Protein Synaptotagmin-1 / Synaptotagmin I / SytI / p65


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
Synaptotagmin-1 / Synaptotagmin I / SytI / p65


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
Vesicle-associated membrane protein 2 / VAMP-2 / Synaptobrevin-2


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
Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


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
Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa 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
Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa 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 / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: 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
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: Situs / Category: model fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 78.48 ° / Axial rise/subunit: 7.3 Å / Axial symmetry: C1
3D reconstructionResolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2082 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 5CCI

5cci


Accession code: 5CCI / Source name: PDB / Type: experimental model

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