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- PDB-7udc: cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex... -
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Basic information
Entry | Database: PDB / ID: 7udc | |||||||||||||||||||||
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Title | cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex class1 | |||||||||||||||||||||
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![]() | EXOCYTOSIS / Munc18 / syntaxin / synaptobrevin / SNARE / membrane fusion / neurotransmitter release | |||||||||||||||||||||
Function / homology | ![]() 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 / Toxicity of tetanus toxin (tetX) / developmental process involved in reproduction / 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 / Toxicity of tetanus toxin (tetX) / developmental process involved in reproduction / 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) / 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 / zymogen granule membrane / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulation of synaptic vesicle priming / Dopamine Neurotransmitter Release Cycle / regulated exocytosis / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / negative regulation of synaptic transmission, GABAergic / response to gravity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / platelet degranulation / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / Dopamine Neurotransmitter Release Cycle / neuromuscular synaptic transmission / synaptic vesicle maturation / Norepinephrine Neurotransmitter Release Cycle / eosinophil degranulation / vesicle docking / 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 / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / Golgi to plasma membrane protein transport / platelet alpha granule / neurotransmitter secretion / ATP-dependent protein binding / protein localization to membrane / neuron projection terminus / vesicle docking involved in exocytosis / presynaptic cytosol / neurotransmitter transport / Sensory processing of sound by inner hair cells of the cochlea / insulin secretion / long-term synaptic depression / syntaxin binding / parallel fiber to Purkinje cell synapse / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / clathrin-coated vesicle / synaptic vesicle priming / Lysosome Vesicle Biogenesis / Other interleukin signaling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Golgi Associated Vesicle Biogenesis / myosin binding / Insulin processing / exocytosis / positive regulation of exocytosis / synaptic vesicle exocytosis / modulation of excitatory postsynaptic potential / phospholipase binding / positive regulation of excitatory postsynaptic potential / protein sumoylation / synaptic vesicle endocytosis / endomembrane system Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||||||||
![]() | Rizo, J. / Bai, X. / Stepien, K.P. / Xu, J. / Zhang, X. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 196 KB | Display | ![]() |
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PDB format | ![]() | 147 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 26456MC ![]() 7udbC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 68714.883 Da / Num. of mol.: 1 / Mutation: D326K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 29221.541 Da / Num. of mol.: 1 / Mutation: C145A, L165A, E166A, L205C Source method: isolated from a genetically manipulated source 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 Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 6645.386 Da / Num. of mol.: 1 / Mutation: Q36C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
Sequence details | An 8 residue polyalanine stretch was modeled between I149 and A178 of chain B entity Syntaxin-1A. ...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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: ternary complex of Munc18-1 bound to syntaxin-1A and a SNARE motif of synaptobrevin 2 Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Conc.: 7.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1600 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 7401 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 30 |
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Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5819182 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 331649 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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