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- EMDB-9103: The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9103 | |||||||||
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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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![]() | SNARE / NSF / SNAP / ATPase / AAA / disassembly / synapse / membrane fusion / exocytosis / HYDROLASE | |||||||||
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 / axonogenesis / SNARE binding / filopodium / locomotory behavior / PDZ domain binding / long-term synaptic potentiation / intracellular protein transport / trans-Golgi network / potassium ion transport / 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 / cytoskeleton / endosome / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | White KI / Zhao M | |||||||||
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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 35.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.1 KB 20.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.1 KB | Display | ![]() |
Images | ![]() | 31.2 KB | ||
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() | 43.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mdpMC ![]() 9100C ![]() 9101C ![]() 9102C ![]() 6mdmC ![]() 6mdnC ![]() 6mdoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | The unsharpened map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: The sharpened map.
File | emd_9103_additional.map | ||||||||||||
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Annotation | The sharpened map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : 20S supercomplex consisting of soluble neuronal SNARE complex, al...
Entire | Name: 20S supercomplex consisting of soluble neuronal SNARE complex, alpha-SNAP, and N-ethylmaleimide sensitive factor (NSF) |
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Components |
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-Supramolecule #1: 20S supercomplex consisting of soluble neuronal SNARE complex, al...
Supramolecule | Name: 20S supercomplex consisting of soluble neuronal SNARE complex, alpha-SNAP, and N-ethylmaleimide sensitive factor (NSF) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 23.625 KDa |
-Supramolecule #2: N-ethylmaleimide sensitive factor
Supramolecule | Name: N-ethylmaleimide sensitive factor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Synaptosomal-associated protein 25
Supramolecule | Name: Synaptosomal-associated protein 25 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Vesicle-fusing ATPase
Macromolecule | Name: Vesicle-fusing ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 85.509227 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGHHHHHHDY DIPTTENLYF QGAHMAGRSM QAARCPTDEL SLSNCAVVSE KDYQSGQHVI VRTSPNHKYI FTLRTHPSVV PGSVAFSLP QRKWAGLSIG QEIEVALYSF DKAKQCIGTM TIEIDFLQKK NIDSNPYDTD KMAAEFIQQF NNQAFSVGQQ L VFSFNDKL ...String: MGHHHHHHDY DIPTTENLYF QGAHMAGRSM QAARCPTDEL SLSNCAVVSE KDYQSGQHVI VRTSPNHKYI FTLRTHPSVV PGSVAFSLP QRKWAGLSIG QEIEVALYSF DKAKQCIGTM TIEIDFLQKK NIDSNPYDTD KMAAEFIQQF NNQAFSVGQQ L VFSFNDKL FGLLVKDIEA MDPSILKGEP ASGKRQKIEV GLVVGNSQVA FEKAENSSLN LIGKAKTKEN RQSIINPDWN FE KMGIGGL DKEFSDIFRR AFASRVFPPE IVEQMGCKHV KGILLYGPPG CGKTLLARQI GKMLNAREPK VVNGPEILNK YVG ESEANI RKLFADAEEE QRRLGANSGL HIIIFDEIDA ICKQRGSMAG STGVHDTVVN QLLSKIDGVE QLNNILVIGM TNRP DLIDE ALLRPGRLEV KMEIGLPDEK GRLQILHIHT ARMRGHQLLS ADVDIKELAV ETKNFSGAEL EGLVRAAQST AMNRH IIAS TKVEVDMEKA ESLQVTRGDF LASLENDIKP AFGTNQEDYA SYIMNGIIKW GDPVTRVLDD GELLVQQTKN SDRTPL VSV LLEGPPHSGK TALAAKIAEE SNFPFIKICS PDKMIGFSET AKCQAMKKIF DDAYKSQLSC VVVDDIERLL DYVPIGP RF SNLVLQALLV LLKKAPPQGR KLLIIGTTSR KDVLQEMEML NAFSTTIHVP NIATGEQLLE ALELLGNFKD KERTTIAQ Q VKGKKVWIGI KKLLMLIEMS LQMDPEYRVR KFLALLREEG ASPLDFD UniProtKB: Vesicle-fusing ATPase |
-Macromolecule #2: Synaptosomal-associated protein 25
Macromolecule | Name: Synaptosomal-associated protein 25 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.512387 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MASMAEDADM RNELEEMQRR ADQLADESLE STRRMLQLVE ESKDAGIRTL VMLDEQGEQL DRVEEGMNHI NQDMKEAEKN LKDLGKCCG LFICPCNKLK SSDAYKKAWG NNQDGVVASQ PARVVDEREQ MAISGGFIRR VTNDARENEM DENLEQVSGI I GNLRHMAL ...String: MASMAEDADM RNELEEMQRR ADQLADESLE STRRMLQLVE ESKDAGIRTL VMLDEQGEQL DRVEEGMNHI NQDMKEAEKN LKDLGKCCG LFICPCNKLK SSDAYKKAWG NNQDGVVASQ PARVVDEREQ MAISGGFIRR VTNDARENEM DENLEQVSGI I GNLRHMAL DMGNEIDTQN RQIDRIMEKA DSNKTRIDEA NQRATKMLG UniProtKB: Synaptosomal-associated protein 25 |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 9 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 15 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK I / Details: Blot for 3.5 seconds before plunging.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 2-40 / Number grids imaged: 2 / Number real images: 5418 / Average exposure time: 10.0 sec. / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen 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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-6mdp: |