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- EMDB-26455: Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-26455
TitleCryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2
Map dataCryo-EM map of synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 1
Sample
  • Complex: ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE motif of synaptobrevin 2
    • Protein or peptide: Syntaxin-binding protein 1
    • Protein or peptide: Syntaxin-1A
    • Protein or peptide: Synaptobrevin-2
KeywordsMunc18 / syntaxin / synaptobrevin / SNARE / membrane fusion / neurotransmitter release / EXOCYTOSIS
Function / homology
Function and homology information


: / regulation of acrosomal vesicle exocytosis / positive regulation of synaptic vesicle priming / evoked neurotransmitter secretion / axon target recognition / negative regulation of SNARE complex assembly / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / developmental process involved in reproduction / regulation of delayed rectifier potassium channel activity ...: / regulation of acrosomal vesicle exocytosis / positive regulation of synaptic vesicle priming / evoked neurotransmitter secretion / axon target recognition / negative regulation of SNARE complex assembly / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / developmental process involved in reproduction / regulation of delayed rectifier potassium channel activity / regulation of vesicle fusion / positive regulation of mast cell degranulation / myosin head/neck binding / Lysosome Vesicle Biogenesis / zymogen granule membrane / positive regulation of glutamate secretion, neurotransmission / storage vacuole / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / platelet degranulation / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / presynaptic dense core vesicle exocytosis / extrinsic component of presynaptic membrane / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / synaptic vesicle maturation / GABA synthesis, release, reuptake and degradation / : / positive regulation of catecholamine secretion / positive regulation of norepinephrine secretion / hormone secretion / Dopamine Neurotransmitter Release Cycle / eosinophil degranulation / regulation of synaptic vesicle priming / regulated exocytosis / Golgi Associated Vesicle Biogenesis / : / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / calcium-ion regulated exocytosis / presynaptic active zone cytoplasmic component / SNARE complex disassembly / positive regulation of calcium ion-dependent exocytosis / positive regulation of intracellular protein transport / positive regulation of neurotransmitter secretion / regulation of vesicle-mediated transport / : / positive regulation of vesicle fusion / chloride channel inhibitor activity / secretion by cell / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / Clathrin-mediated endocytosis / SNARE complex / neuromuscular synaptic transmission / platelet alpha granule / SNAP receptor activity / vesicle fusion / actomyosin / LGI-ADAM interactions / negative regulation of synaptic transmission, GABAergic / Golgi to plasma membrane protein transport / response to cholesterol / neurotransmitter secretion / ATP-dependent protein binding / long-term synaptic depression / clathrin-coated vesicle / syntaxin binding / insulin secretion / syntaxin-1 binding / protein localization to membrane / regulation of synaptic vesicle recycling / myosin binding / SNARE complex assembly / synaptic vesicle priming / neuron projection terminus / establishment of localization in cell / response to gravity / exocytosis / parallel fiber to Purkinje cell synapse / neurotransmitter transport / positive regulation of exocytosis / synaptic vesicle exocytosis / modulation of excitatory postsynaptic potential / protein sumoylation / response to glucose / postsynaptic cytosol / negative regulation of protein-containing complex assembly / synaptic vesicle endocytosis / calcium channel inhibitor activity / presynaptic cytosol / phospholipase binding / vesicle-mediated transport / phagocytic vesicle / presynaptic active zone membrane / endomembrane system / secretory granule / acrosomal vesicle
Similarity search - Function
Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Syntaxin ...Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Syntaxin / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / 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
Similarity search - Domain/homology
Syntaxin-1A / Syntaxin-binding protein 1 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRizo J / Bai X / Stepien KP / Xu J / Zhang X
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35 NS097333 United States
Robert A. Welch FoundationI-1304 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD030312-01 United States
Robert A. Welch FoundationI-1441 United States
Robert A. Welch FoundationI-1702 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130289 United States
CitationJournal: Sci Adv / Year: 2022
Title: SNARE assembly enlightened by cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex.
Authors: Karolina P Stepien / Junjie Xu / Xuewu Zhang / Xiao-Chen Bai / Josep Rizo /
Abstract: Munc18-1 forms a template to organize assembly of the neuronal SNARE complex that triggers neurotransmitter release, binding first to a closed conformation of syntaxin-1 where its amino-terminal ...Munc18-1 forms a template to organize assembly of the neuronal SNARE complex that triggers neurotransmitter release, binding first to a closed conformation of syntaxin-1 where its amino-terminal region interacts with the SNARE motif, and later binding to synaptobrevin. However, the mechanism of SNARE complex assembly remains unclear. Here, we report two cryo-EM structures of Munc18-1 bound to cross-linked syntaxin-1 and synaptobrevin. The structures allow visualization of how syntaxin-1 opens and reveal how part of the syntaxin-1 amino-terminal region can help nucleate interactions between the amino termini of the syntaxin-1 and synaptobrevin SNARE motifs, while their carboxyl termini bind to distal sites of Munc18-1. These observations, together with mutagenesis, SNARE complex assembly experiments, and fusion assays with reconstituted proteoliposomes, support a model whereby these interactions are critical to initiate SNARE complex assembly and multiple energy barriers enable diverse mechanisms for exquisite regulation of neurotransmitter release.
History
DepositionMar 18, 2022-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26455.png

Downloads & links

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Map

FileDownload / File: emd_26455.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 180 pix.
= 194.4 Å		1.08 Å/pix.
x 180 pix.
= 194.4 Å		1.08 Å/pix.
x 180 pix.
= 194.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.34721613 - 0.56915826
Average (Standard dev.)0.0004786197 (±0.013151482)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 194.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM map of synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 1, unfiltered...

Fileemd_26455_half_map_1.map
AnnotationCryo-EM map of synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 1, unfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 1, unfiltered...

Fileemd_26455_half_map_2.map
AnnotationCryo-EM map of synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 1, unfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE moti...

EntireName: ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE motif of synaptobrevin 2
Components
  • Complex: ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE motif of synaptobrevin 2
    • Protein or peptide: Syntaxin-binding protein 1
    • Protein or peptide: Syntaxin-1A
    • Protein or peptide: Synaptobrevin-2

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Supramolecule #1: ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE moti...

SupramoleculeName: ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE motif of synaptobrevin 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Syntaxin-binding protein 1

MacromoleculeName: Syntaxin-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 68.714883 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSPGISGGGG GIHMAPIGLK AVVGEKIMHD VIKKVKKKGE WKVLVVDQLS MRMLSSCCKM TDIMTEGITI VEDINKRREP LPSLEAVYL ITPSEKSVHS LISDFKDPPT AKYRAAHVFF TDSCPDALFN ELVKSRAAKV IKTLTEINIA FLPYESQVYS L DSADSFQS ...String:
GSPGISGGGG GIHMAPIGLK AVVGEKIMHD VIKKVKKKGE WKVLVVDQLS MRMLSSCCKM TDIMTEGITI VEDINKRREP LPSLEAVYL ITPSEKSVHS LISDFKDPPT AKYRAAHVFF TDSCPDALFN ELVKSRAAKV IKTLTEINIA FLPYESQVYS L DSADSFQS FYSPHKAQMK NPILERLAEQ IATLCATLKE YPAVRYRGEY KDNALLAQLI QDKLDAYKAD DPTMGEGPDK AR SQLLILD RGFDPSSPVL HELTFQAMSY DLLPIENDVY KYETSGIGEA RVKEVLLDED DDLWIALRHK HIAEVSQEVT RSL KDFSSS KRMNTGEKTT MRKLSQMLKK MPQYQKELSK YSTHLHLAED CMKHYQGTVD KLCRVEQDLA MGTDAEGEKI KDPM RAIVP ILLDANVSTY DKIRIILLYI FLKNGITEEN LNKLIQHAQI PPEDSEIITN MAHLGVPIVT DSTLRRRSKP ERKER ISEQ TYQLSRWTPI IKDIMEDTIE DKLDTKHYPY ISTRSSASFS TTAVSARYGH WHKNKAPGEY RSGPRLIIFI LGGVSL NEM RCAYEVTQAN GKWEVLIGST HILTPQKLLD TLKKLNKTDE EISS

UniProtKB: Syntaxin-binding protein 1

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Macromolecule #2: Syntaxin-1A

MacromoleculeName: Syntaxin-1A / type: protein_or_peptide / ID: 2
Details: An 8 residue polyalanine stretch was modeled between I149 and A178 of chain B entity Syntaxin-1A. Side chains in this region were not visible and residue numbers are tentative. While ...Details: An 8 residue polyalanine stretch was modeled between I149 and A178 of chain B entity Syntaxin-1A. Side chains in this region were not visible and residue numbers are tentative. While processing in OneDep the polyalanine sequence was updated to 162-SEEAADML-169
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 29.221541 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSKDRTQELR TAKDSDDDDD VTVTVDRDRF MDEFFEQVEE IRGFIDKIAE NVEEVKRKHS AILASPNPDE KTKEELEELM SDIKKTANK VRSKLKSIEQ SIEQEEGLNR SSADLRIRKT QHSTLSRKFV EVMSEYNATQ SDYRERAKGR IQRQLEITGR T TTSEEAAD ...String:
GSKDRTQELR TAKDSDDDDD VTVTVDRDRF MDEFFEQVEE IRGFIDKIAE NVEEVKRKHS AILASPNPDE KTKEELEELM SDIKKTANK VRSKLKSIEQ SIEQEEGLNR SSADLRIRKT QHSTLSRKFV EVMSEYNATQ SDYRERAKGR IQRQLEITGR T TTSEEAAD MLESGNPAIF ASGIIMDSSI SKQALSEIET RHSEIIKCEN SIRELHDMFM DMAMLVESQG EMIDRIEYNV EH AVDYVER AVSDTKK

UniProtKB: Syntaxin-1A

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Macromolecule #3: Synaptobrevin-2

MacromoleculeName: Synaptobrevin-2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 6.645386 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSMWNRRLQQ TCAQVDEVVD IMRVNVDKVL ERDQKLSELD DRADALQAGA SQFETSAAK

UniProtKB: Vesicle-associated membrane protein 2

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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

Concentration7.5 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 7401 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5819182
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: From RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 345463
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationNumber classes: 6 / Software - Name: RELION

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