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- PDB-6mdp: The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus... -
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Basic information
Entry | Database: PDB / ID: 6mdp | ||||||
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Title | The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus within the 20S supercomplex (focused refinement on D1/D2 rings, class 2) | ||||||
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![]() | HYDROLASE / SNARE / NSF / SNAP / ATPase / AAA / disassembly / synapse / membrane fusion / exocytosis | ||||||
Function / homology | ![]() BLOC-1 complex / SNARE complex disassembly / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / 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 / Glutamate Neurotransmitter Release Cycle ...BLOC-1 complex / SNARE complex disassembly / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / 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 / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / presynaptic dense core vesicle exocytosis / ribbon synapse / regulation of establishment of protein localization / calcium ion-regulated exocytosis of neurotransmitter / ATP-dependent protein disaggregase activity / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / positive regulation of hormone secretion / neurotransmitter secretion / Golgi stack / neurotransmitter receptor internalization / vesicle-fusing ATPase / syntaxin-1 binding / SNARE complex assembly / Neutrophil degranulation / synaptic vesicle priming / endosomal transport / regulation of synapse assembly / myosin binding / positive regulation of receptor recycling / regulation of neuron projection development / exocytosis / voltage-gated potassium channel activity / synaptic vesicle exocytosis / associative learning / long-term memory / axonal growth cone / presynaptic active zone membrane / voltage-gated potassium channel complex / somatodendritic compartment / ionotropic glutamate receptor binding / photoreceptor inner segment / potassium ion transport / axonogenesis / SNARE binding / filopodium / locomotory behavior / PDZ domain binding / long-term synaptic potentiation / intracellular protein transport / trans-Golgi network / positive regulation of insulin secretion / terminal bouton / neuron differentiation / positive regulation of protein catabolic process / calcium-dependent protein binding / actin cytoskeleton / synaptic vesicle / lamellipodium / presynapse / presynaptic membrane / cell cortex / midbody / growth cone / transmembrane transporter binding / postsynapse / endosome / cytoskeleton / neuron projection / protein domain specific binding / axon / neuronal cell body / lipid binding / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | White, K.I. / Zhao, M. / Brunger, A.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural principles of SNARE complex recognition by the AAA+ protein NSF. Authors: K Ian White / Minglei Zhao / Ucheor B Choi / Richard A Pfuetzner / Axel T Brunger / ![]() Abstract: The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (-ethylmaleimide sensitive ...The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (-ethylmaleimide sensitive factor) and an adaptor protein, SNAP (soluble NSF attachment protein), disassemble the SNARE complex. We report electron-cryomicroscopy structures of the complex of NSF, αSNAP, and the full-length soluble neuronal SNARE complex (composed of syntaxin-1A, synaptobrevin-2, SNAP-25A) in the presence of ATP under non-hydrolyzing conditions at ~3.9 Å resolution. These structures reveal electrostatic interactions by which two αSNAP molecules interface with a specific surface of the SNARE complex. This interaction positions the SNAREs such that the 15 N-terminal residues of SNAP-25A are loaded into the D1 ring pore of NSF via a spiral pattern of interactions between a conserved tyrosine NSF residue and SNAP-25A backbone atoms. This loading process likely precedes ATP hydrolysis. Subsequent ATP hydrolysis then drives complete disassembly. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 959.1 KB | Display | ![]() |
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PDB format | ![]() | 788.2 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9103MC ![]() 9100C ![]() 9101C ![]() 9102C ![]() 6mdmC ![]() 6mdnC ![]() 6mdoC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 85509.227 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 23512.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-ATP / |
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-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
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Buffer solution | pH: 8 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: Blot for 3.5 seconds before plunging. |
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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: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 58 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 5418 |
Image scans | Movie frames/image: 40 / Used frames/image: 2-40 |
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Processing
EM software |
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CTF correction | Details: CTF correction was carried out in Relion with reconstruction step. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 475680 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 184555 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3J96 Accession code: 3J96 / Source name: PDB / Type: experimental model |