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- PDB-6ip1: alpha-SNAP-SNARE subcomplex in the whole 20S complex -

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Basic information

Entry
Database: PDB / ID: 6ip1
Titlealpha-SNAP-SNARE subcomplex in the whole 20S complex
Components
  • (Synaptosomal-associated protein 25) x 2
  • Alpha-soluble NSF attachment protein
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsMEMBRANE PROTEIN / membrane fusion / ATPase
Function / homology
Function and homology information


exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / soluble NSF attachment protein activity / BLOC-1 complex / myosin head/neck binding / Lysosome Vesicle Biogenesis / zymogen granule membrane / positive regulation of glutamate secretion, neurotransmission / synaptic vesicle fusion to presynaptic active zone membrane ...exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / soluble NSF attachment protein activity / BLOC-1 complex / myosin head/neck binding / Lysosome Vesicle Biogenesis / zymogen granule membrane / positive regulation of glutamate secretion, neurotransmission / synaptic vesicle fusion to presynaptic active zone membrane / storage vacuole / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / presynaptic dense core vesicle exocytosis / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of catecholamine secretion / positive regulation of norepinephrine secretion / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / eosinophil degranulation / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming / regulated exocytosis / vesicle-mediated transport in synapse / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / short-term synaptic potentiation / regulation of establishment of protein localization / SNARE complex disassembly / positive regulation of calcium ion-dependent exocytosis / ribbon synapse / positive regulation of intracellular protein transport / regulation of vesicle-mediated transport / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / positive regulation of vesicle fusion / chloride channel inhibitor activity / secretion by cell / Clathrin-mediated endocytosis / calcium-ion regulated exocytosis / SNARE complex / regulation of exocytosis / SNAP receptor activity / vesicle fusion / actomyosin / hormone secretion / LGI-ADAM interactions / positive regulation of synaptic plasticity / positive regulation of hormone secretion / Golgi to plasma membrane protein transport / ATP-dependent protein binding / response to cholesterol / neurotransmitter secretion / clathrin-coated vesicle / regulation of synaptic vesicle cycle / syntaxin binding / protein localization to membrane / syntaxin-1 binding / Neutrophil degranulation / regulation of synaptic vesicle recycling / insulin secretion / endosomal transport / myosin binding / positive regulation of neurotransmitter secretion / regulation of synapse assembly / neurotransmitter transport / SNARE complex assembly / response to gravity / regulation of neuron projection development / synaptic vesicle priming / neuron projection terminus / exocytosis / positive regulation of exocytosis / protein sumoylation / modulation of excitatory postsynaptic potential / synaptic vesicle exocytosis / associative learning / voltage-gated potassium channel activity / synaptic vesicle endocytosis / postsynaptic cytosol / response to glucose / long-term memory / axonal growth cone / calcium channel inhibitor activity / vesicle-mediated transport / somatodendritic compartment / voltage-gated potassium channel complex / photoreceptor inner segment / presynaptic active zone membrane / endomembrane system / axonogenesis / secretory granule / acrosomal vesicle
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / NSF attachment protein / Soluble NSF attachment protein, SNAP / Synaptobrevin signature. / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / NSF attachment protein / Soluble NSF attachment protein, SNAP / Synaptobrevin signature. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NAPA protein / Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 2 / Alpha-soluble NSF attachment protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHuang, X. / Sun, S. / Wang, X. / Fan, F. / Zhou, Q. / Sui, S.F.
CitationJournal: Sci Adv / Year: 2019
Title: Mechanistic insights into the SNARE complex disassembly.
Authors: Xuan Huang / Shan Sun / Xiaojing Wang / Fenghui Fan / Qiang Zhou / Shan Lu / Yong Cao / Qiu-Wen Wang / Meng-Qiu Dong / Jun Yao / Sen-Fang Sui /
Abstract: NSF (-ethylmaleimide-sensitive factor) and α-SNAP (α-soluble NSF attachment protein) bind to the SNARE (soluble NSF attachment protein receptor) complex, the minimum machinery to mediate membrane ...NSF (-ethylmaleimide-sensitive factor) and α-SNAP (α-soluble NSF attachment protein) bind to the SNARE (soluble NSF attachment protein receptor) complex, the minimum machinery to mediate membrane fusion, to form a 20S complex, which disassembles the SNARE complex for reuse. We report the cryo-EM structures of the α-SNAP-SNARE subcomplex and the NSF-D1D2 domain in the 20S complex at 3.9- and 3.7-Å resolutions, respectively. Combined with the biochemical and electrophysiological analyses, we find that α-SNAPs use R116 through electrostatic interactions and L197 through hydrophobic interactions to apply force mainly on two positions of the VAMP protein to execute disassembly process. Furthermore, we define the interaction between the amino terminus of the SNARE helical bundle and the pore loop of the NSF-D1 domain and demonstrate its essential role as a potential anchor for SNARE complex disassembly. Our studies provide a rotation model of α-SNAP-mediated disassembly of the SNARE complex.
History
DepositionNov 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Alpha-soluble NSF attachment protein
F: Alpha-soluble NSF attachment protein
G: Alpha-soluble NSF attachment protein
H: Alpha-soluble NSF attachment protein


Theoretical massNumber of molelcules
Total (without water)199,9448
Polymers199,9448
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area24560 Å2
ΔGint-124 kcal/mol
Surface area69450 Å2

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Components

#1: Protein Vesicle-associated membrane protein 2 / VAMP-2


Mass: 10550.823 Da / Num. of mol.: 1 / Fragment: UNP residues 1-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63045
#2: Protein Syntaxin-1A


Mass: 29363.736 Da / Num. of mol.: 1 / Fragment: UNP residues 2-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a / Production host: Escherichia coli (E. coli) / References: UniProt: P32851
#3: Protein Synaptosomal-associated protein 25 / SNAP-25


Mass: 11571.022 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25 / Production host: Escherichia coli (E. coli) / References: UniProt: P60881
#4: Protein Synaptosomal-associated protein 25 / SNAP-25


Mass: 9277.316 Da / Num. of mol.: 1 / Fragment: UNP residues 126-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25 / Production host: Escherichia coli (E. coli) / References: UniProt: P60881
#5: Protein
Alpha-soluble NSF attachment protein / NAPA protein


Mass: 34795.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: NAPA / Production host: Escherichia coli (E. coli) / References: UniProt: A5D7S0, UniProt: P81125*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: alpha-SNAP-SNARE subcomplex in the whole 20S complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97910 / Symmetry type: POINT

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