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Yorodumi- EMDB-9102: The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus... -
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-Basic information
Entry | Database: EMDB / ID: EMD-9102 | |||||||||
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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 1) | |||||||||
Map data | Unsharpened map. | |||||||||
Sample |
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Keywords | SNARE / NSF / SNAP / ATPase / AAA / disassembly / synapse / membrane fusion / exocytosis / HYDROLASE | |||||||||
Function / homology | Function and homology information BLOC-1 complex / SNARE complex disassembly / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / 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 / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / 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 / regulation of establishment of protein localization / presynaptic dense core vesicle exocytosis / ribbon synapse / calcium ion-regulated exocytosis of neurotransmitter / ATP-dependent protein disaggregase activity / SNARE complex / SNAP receptor activity / neurotransmitter secretion / positive regulation of hormone secretion / neurotransmitter receptor internalization / vesicle-fusing ATPase / syntaxin-1 binding / SNARE complex assembly / synaptic vesicle priming / Neutrophil degranulation / regulation of synapse assembly / endosomal transport / myosin binding / positive regulation of receptor recycling / regulation of neuron projection development / exocytosis / synaptic vesicle exocytosis / voltage-gated potassium channel activity / associative learning / long-term memory / voltage-gated potassium channel complex / axonal growth cone / presynaptic active zone membrane / somatodendritic compartment / ionotropic glutamate receptor binding / photoreceptor inner segment / axonogenesis / SNARE binding / locomotory behavior / filopodium / long-term synaptic potentiation / PDZ domain binding / intracellular protein transport / trans-Golgi network / potassium ion transport / terminal bouton / positive regulation of insulin secretion / neuron differentiation / positive regulation of protein catabolic process / calcium-dependent protein binding / synaptic vesicle / actin cytoskeleton / presynapse / lamellipodium / presynaptic membrane / cell cortex / midbody / growth cone / postsynapse / transmembrane transporter binding / cytoskeleton / endosome / neuron projection / axon / protein domain specific binding / neuronal cell body / glutamatergic synapse / lipid binding / synapse / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / Cricetulus griseus (Chinese hamster) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | White KI / Zhao M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2018 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9102.map.gz | 35.5 MB | EMDB map data format | |
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Header (meta data) | emd-9102-v30.xml emd-9102.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9102_fsc.xml | 8.1 KB | Display | FSC data file |
Images | emd_9102.png | 31.6 KB | ||
Filedesc metadata | emd-9102.cif.gz | 7.1 KB | ||
Others | emd_9102_additional.map.gz | 43.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9102 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9102 | HTTPS FTP |
-Related structure data
Related structure data | 6mdoMC 9100C 9101C 9103C 6mdmC 6mdnC 6mdpC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9102.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 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: Sharpened map.
File | emd_9102_additional.map | ||||||||||||
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Annotation | Sharpened map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-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: Rattus norvegicus (Norway rat) |
-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: Rattus norvegicus (Norway rat) |
-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: Cricetulus griseus (Chinese hamster) |
Molecular weight | Theoretical: 85.509227 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 23.512387 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 9 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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: 200 / 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.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-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-6mdo: |