+Open data
-Basic information
Entry | Database: PDB / ID: 1sfc | ||||||
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Title | NEURONAL SYNAPTIC FUSION COMPLEX | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / MEMBRANE FUSION PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / 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 ...trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / 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 / Lysosome Vesicle Biogenesis / 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 / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulation of synaptic vesicle priming / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulated exocytosis / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / regulation of establishment of protein localization / storage vacuole / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / eosinophil degranulation / vesicle docking / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / regulation of exocytosis / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / Golgi to plasma membrane protein transport / positive regulation of hormone secretion / neurotransmitter secretion / neurotransmitter receptor internalization / ATP-dependent protein binding / protein localization to membrane / neuron projection terminus / regulation of synaptic vesicle recycling / neurotransmitter transport / insulin secretion / syntaxin binding / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / clathrin-coated vesicle / Neutrophil degranulation / synaptic vesicle priming / endosomal transport / regulation of synapse assembly / postsynaptic cytosol / myosin binding / regulation of neuron projection development / exocytosis / voltage-gated potassium channel activity / positive regulation of exocytosis / synaptic vesicle exocytosis / modulation of excitatory postsynaptic potential / associative learning / positive regulation of excitatory postsynaptic potential / protein sumoylation / synaptic vesicle endocytosis / endomembrane system / calcium channel inhibitor activity / long-term memory / response to glucose / axonal growth cone / presynaptic active zone membrane / voltage-gated potassium channel complex / vesicle-mediated transport / somatodendritic compartment / photoreceptor inner segment / axonogenesis / acrosomal vesicle / SNARE binding / secretory granule / filopodium / locomotory behavior / establishment of localization in cell / long-term synaptic potentiation / kinase binding / intracellular protein transport Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å | ||||||
Authors | Sutton, R.B. / Brunger, A.T. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 A resolution. Authors: Sutton, R.B. / Fasshauer, D. / Jahn, R. / Brunger, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sfc.cif.gz | 187.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sfc.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 1sfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sfc_validation.pdf.gz | 552 KB | Display | wwPDB validaton report |
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Full document | 1sfc_full_validation.pdf.gz | 598 KB | Display | |
Data in XML | 1sfc_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 1sfc_validation.cif.gz | 50.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/1sfc ftp://data.pdbj.org/pub/pdb/validation_reports/sf/1sfc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 6 molecules AEIBFJ
#1: Protein | Mass: 10530.938 Da / Num. of mol.: 3 / Fragment: PROTEOLYTICALLY PROTECTED FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: NEURON / Plasmid: PET28-A / Production host: Escherichia coli (E. coli) / References: UniProt: P63045 #2: Protein | Mass: 9603.944 Da / Num. of mol.: 3 / Fragment: PROTEOLYTICALLY PROTECTED FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: NEURON / Plasmid: PET28-A / Production host: Escherichia coli (E. coli) / References: UniProt: P32851 |
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-PROTEIN (SNAP- ... , 2 types, 6 molecules CGKDHL
#3: Protein | Mass: 9662.756 Da / Num. of mol.: 3 / Fragment: PROTEOLYTICALLY PROTECTED FRAGMENT Source method: isolated from a genetically manipulated source Details: ISOFORM SNAP-25'B' / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: NEURON / Plasmid: PET28-A / Production host: Escherichia coli (E. coli) / References: UniProt: P60881 #4: Protein | Mass: 9861.957 Da / Num. of mol.: 3 / Fragment: PROTEOLYTICALLY PROTECTED FRAGMENT Source method: isolated from a genetically manipulated source Details: ISOFORM SNAP-25'B' / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: NEURON / Plasmid: PET28-A / Production host: Escherichia coli (E. coli) / References: UniProt: P60881 |
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-Non-polymers , 3 types, 39 molecules
#5: Chemical | ChemComp-SR / #6: Chemical | ChemComp-MPD / ( #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 54.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 35% MPD, 5% PEG350(MME), 25MM TRIS PH 7.0,. 70MM SRCL2, 250MM UREA, 7MM SARKOSYL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 29 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.0332,0.9797,1.0688,0.9801,0.9795,0.9800 | |||||||||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: May 15, 1998 / Details: BENT MIRROR | |||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→50 Å / Num. obs: 42980 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 10 Å2 / Rsym value: 0.079 / Net I/σ(I): 17.4 | |||||||||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 7.6 / Rsym value: 0.309 / % possible all: 98.8 | |||||||||||||||||||||
Reflection | *PLUS Num. measured all: 309408 / Rmerge(I) obs: 0.079 | |||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.329 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 5215518.75 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.46 Å2 / ksol: 0.386 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 45.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.367 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.337 |