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Yorodumi- EMDB-26456: cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26456 | |||||||||||||||||||||
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Title | cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex class1 | |||||||||||||||||||||
Map data | cryo-EM map of a synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 2 | |||||||||||||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / regulation of vesicle fusion / developmental process involved in reproduction / Toxicity of tetanus toxin (tetX) / axon target recognition / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane ...positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / regulation of vesicle fusion / developmental process involved in reproduction / Toxicity of tetanus toxin (tetX) / axon target recognition / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / regulation of delayed rectifier potassium channel activity / Toxicity of botulinum toxin type F (botF) / myosin head/neck binding / Toxicity of botulinum toxin type D (botD) / trans-Golgi Network Vesicle Budding / Other interleukin signaling / extrinsic component of presynaptic membrane / Acetylcholine Neurotransmitter Release Cycle / 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 / Toxicity of botulinum toxin type B (botB) / platelet degranulation / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / zymogen granule membrane / negative regulation of synaptic transmission, GABAergic / Dopamine Neurotransmitter Release Cycle / regulated exocytosis / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / clathrin-sculpted monoamine transport vesicle membrane / response to gravity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Serotonin Neurotransmitter Release Cycle / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / synaptic vesicle maturation / eosinophil degranulation / neuromuscular synaptic transmission / vesicle docking / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / presynaptic active zone cytoplasmic component / Glutamate Neurotransmitter Release Cycle / positive regulation of mast cell degranulation / regulation of vesicle-mediated transport / regulation of exocytosis / LGI-ADAM interactions / calcium-ion regulated exocytosis / hormone secretion / actomyosin / positive regulation of intracellular protein transport / platelet alpha granule / Golgi to plasma membrane protein transport / neurotransmitter secretion / protein localization to membrane / ATP-dependent protein binding / neuron projection terminus / vesicle docking involved in exocytosis / presynaptic cytosol / insulin secretion / Sensory processing of sound by inner hair cells of the cochlea / long-term synaptic depression / parallel fiber to Purkinje cell synapse / neurotransmitter transport / syntaxin-1 binding / syntaxin binding / clathrin-coated vesicle / SNARE complex assembly / positive regulation of neurotransmitter secretion / Lysosome Vesicle Biogenesis / synaptic vesicle priming / Other interleukin signaling / Golgi Associated Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / myosin binding / Insulin processing / exocytosis / modulation of excitatory postsynaptic potential / synaptic vesicle exocytosis / positive regulation of exocytosis / phospholipase binding / protein sumoylation / positive regulation of excitatory postsynaptic potential / synaptic vesicle endocytosis / calcium channel inhibitor activity Similarity search - Function | |||||||||||||||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||||||||
Authors | Rizo J / Bai X / Stepien KP / Xu J / Zhang X | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26456.map.gz | 14.8 MB | EMDB map data format | |
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Header (meta data) | emd-26456-v30.xml emd-26456.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
Images | emd_26456.png | 140.6 KB | ||
Others | emd_26456_half_map_1.map.gz emd_26456_half_map_2.map.gz | 17 MB 17 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26456 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26456 | HTTPS FTP |
-Validation report
Summary document | emd_26456_validation.pdf.gz | 594.3 KB | Display | EMDB validaton report |
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Full document | emd_26456_full_validation.pdf.gz | 593.8 KB | Display | |
Data in XML | emd_26456_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | emd_26456_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26456 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26456 | HTTPS FTP |
-Related structure data
Related structure data | 7udcMC 7udbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26456.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | cryo-EM map of a synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: cryo-EM map of a synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 2,...
File | emd_26456_half_map_1.map | ||||||||||||
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Annotation | cryo-EM map of a synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 2, unfiltered half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM map of a synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 2,...
File | emd_26456_half_map_2.map | ||||||||||||
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Annotation | cryo-EM map of a synaptobrevin-Munc18-1-syntaxin-1 complex, conformation 2, unfiltered half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE moti...
Entire | Name: ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE motif of synaptobrevin 2 |
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Components |
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-Supramolecule #1: ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE moti...
Supramolecule | Name: ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE motif of synaptobrevin 2 type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #1: Syntaxin-binding protein 1
Macromolecule | Name: Syntaxin-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 68.714883 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: Syntaxin-1A
Macromolecule | Name: 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 161-TSEEAADM-168 Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 29.221541 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #3: Synaptobrevin-2
Macromolecule | Name: Synaptobrevin-2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 6.645386 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GSMWNRRLQQ TCAQVDEVVD IMRVNVDKVL ERDQKLSELD DRADALQAGA SQFETSAAK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7.5 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |