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- EMDB-9697: alpha-SNAP-SNARE subcomplex in the whole 20S complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9697
Titlealpha-SNAP-SNARE subcomplex in the whole 20S complex
Map data
Sample
  • Complex: alpha-SNAP-SNARE subcomplex in the whole 20S complex
    • Protein or peptide: Vesicle-associated membrane protein 2
    • Protein or peptide: Syntaxin-1A
    • Protein or peptide: Synaptosomal-associated protein 25
    • Protein or peptide: Synaptosomal-associated protein 25
    • Protein or peptide: Alpha-soluble NSF attachment protein
Keywordsmembrane fusion / ATPase / MEMBRANE PROTEIN
Function / homology
Function and homology information


soluble NSF attachment protein activity / trans-Golgi Network Vesicle Budding / BLOC-1 complex / SNARE complex disassembly / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex ...soluble NSF attachment protein activity / trans-Golgi Network Vesicle Budding / BLOC-1 complex / SNARE complex disassembly / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Lysosome Vesicle Biogenesis / positive regulation of norepinephrine secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / zymogen granule membrane / regulated exocytosis / ribbon synapse / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / storage vacuole / regulation of establishment of protein localization / response to gravity / vesicle-mediated transport in synapse / positive regulation of calcium ion-dependent exocytosis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / calcium ion-regulated exocytosis of neurotransmitter / vesicle fusion / eosinophil degranulation / vesicle docking / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / LGI-ADAM interactions / calcium-ion regulated exocytosis / hormone secretion / actomyosin / positive regulation of intracellular protein transport / Golgi to plasma membrane protein transport / neurotransmitter secretion / positive regulation of hormone secretion / neurotransmitter receptor internalization / protein localization to membrane / ATP-dependent protein binding / neuron projection terminus / regulation of synaptic vesicle recycling / insulin secretion / syntaxin binding / neurotransmitter transport / syntaxin-1 binding / clathrin-coated vesicle / SNARE complex assembly / vacuolar membrane / positive regulation of neurotransmitter secretion / Neutrophil degranulation / endosomal transport / synaptic vesicle priming / regulation of synapse assembly / postsynaptic cytosol / myosin binding / regulation of neuron projection development / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / associative learning / exocytosis / synaptic vesicle exocytosis / protein sumoylation / positive regulation of excitatory postsynaptic potential / voltage-gated potassium channel activity / synaptic vesicle endocytosis / endomembrane system / calcium channel inhibitor activity / long-term memory / response to glucose / axonal growth cone / voltage-gated potassium channel complex / presynaptic active zone membrane / vesicle-mediated transport / somatodendritic compartment / photoreceptor inner segment / axonogenesis / acrosomal vesicle / SNARE binding / secretory granule / filopodium / synaptic transmission, glutamatergic
Similarity search - Function
NSF attachment protein / Soluble NSF attachment protein, SNAP / Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain ...NSF attachment protein / Soluble NSF attachment protein, SNAP / Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Syntaxin / Synaptobrevin / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Tetratricopeptide-like helical domain superfamily
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 (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHuang X / Sun S
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, 2018-
Header (metadata) releaseApr 24, 2019-
Map releaseApr 24, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ip1
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9697.png

Downloads & links

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Map

FileDownload / File: emd_9697.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 160 pix.
= 209.046 Å		1.31 Å/pix.
x 160 pix.
= 209.046 Å		1.31 Å/pix.
x 160 pix.
= 209.046 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.22644924 - 0.3121678
Average (Standard dev.)0.00133771 (±0.01583507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 209.0464 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.30653751.30653751.3065375
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z209.046209.046209.046
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.2260.3120.001

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Supplemental data

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Sample components

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Entire : alpha-SNAP-SNARE subcomplex in the whole 20S complex

EntireName: alpha-SNAP-SNARE subcomplex in the whole 20S complex
Components
  • Complex: alpha-SNAP-SNARE subcomplex in the whole 20S complex
    • Protein or peptide: Vesicle-associated membrane protein 2
    • Protein or peptide: Syntaxin-1A
    • Protein or peptide: Synaptosomal-associated protein 25
    • Protein or peptide: Synaptosomal-associated protein 25
    • Protein or peptide: Alpha-soluble NSF attachment protein

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Supramolecule #1: alpha-SNAP-SNARE subcomplex in the whole 20S complex

SupramoleculeName: alpha-SNAP-SNARE subcomplex in the whole 20S complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Vesicle-associated membrane protein 2

MacromoleculeName: Vesicle-associated membrane protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 10.550823 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSATAAT VPPAAPAGEG GPPAPPPNLT SNRRLQQTQA QVDEVVDIMR VNVDKVLERD QKLSELDDRA DALQAGASQF ETSAAKLKR KYWWKNLK

UniProtKB: Vesicle-associated membrane protein 2

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Macromolecule #2: Syntaxin-1A

MacromoleculeName: Syntaxin-1A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 29.363736 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSKDRTQELR TAKDSDDDDD VTVTVDRDRF MDEFFEQVEE IRGFIDKIAE NVEEVKRKHS AILASPNPDE KTKEELEELM SDIKKTANK VRSKLKSIEQ SIEQEEGLNR SSADLRIRKT QHSTLSRKFV EVMSEYNATQ SDYRERCKGR IQRQLEITGR T TTSEELED ...String:
GSKDRTQELR TAKDSDDDDD VTVTVDRDRF MDEFFEQVEE IRGFIDKIAE NVEEVKRKHS AILASPNPDE KTKEELEELM SDIKKTANK VRSKLKSIEQ SIEQEEGLNR SSADLRIRKT QHSTLSRKFV EVMSEYNATQ SDYRERCKGR IQRQLEITGR T TTSEELED MLESGNPAIF ASGIIMDSSI SKQALSEIET RHSEIIKLEN SIRELHDMFM DMAMLVESQG EMIDRIEYNV EH AVDYVER AVSDTKK

UniProtKB: Syntaxin-1A

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Macromolecule #3: Synaptosomal-associated protein 25

MacromoleculeName: Synaptosomal-associated protein 25 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 11.571022 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSMAEDADMR NELEEMQRRA DQLADESLES TRRMLQLVEE SKDAGIRTLV MLDEQGEQLE RIEEGMDQIN KDMKEAEKNL TDLGKFCGL CVCPCNKLKS SDA

UniProtKB: Synaptosomal-associated protein 25

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Macromolecule #4: Synaptosomal-associated protein 25

MacromoleculeName: Synaptosomal-associated protein 25 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 9.277316 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSQMAISGGF IRRVTNDARE NEMDENLEQV SGIIGNLRHM ALDMGNEIDT QNRQIDRIME KADSNKTRID EANQRATKML GSG

UniProtKB: Synaptosomal-associated protein 25

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Macromolecule #5: Alpha-soluble NSF attachment protein

MacromoleculeName: Alpha-soluble NSF attachment protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 34.795332 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMRGSHHHH HHGSMDNSGK EAEAMALLAE AERKVKNSQS FFSGLFGGSS KIEEACEIYA RAANMFKMAK NWSAAGSAFC QAAQLHLQL QSKHDAATCF VDAGNAFKKA DPQEAINCLM RAIEIYTDMG RFTIAAKHHI SIAEIYETEL VDIEKAIAHY E QSADYYKG ...String:
GSMRGSHHHH HHGSMDNSGK EAEAMALLAE AERKVKNSQS FFSGLFGGSS KIEEACEIYA RAANMFKMAK NWSAAGSAFC QAAQLHLQL QSKHDAATCF VDAGNAFKKA DPQEAINCLM RAIEIYTDMG RFTIAAKHHI SIAEIYETEL VDIEKAIAHY E QSADYYKG EESNSSANKC LLKVAGYAAQ LEQYQKAIDI YEQVGTNAMD SPLLKYSAKD YFFKAALCHF CIDMLNAKLA VQ KYEELFP AFSDSRECKL MKKLLEAHEE QNVDSYTEAV KEYDSISRLD QWLTTMLLRI KKTIQGDEED LR

UniProtKB: NAPA protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97910
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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