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Yorodumi- PDB-1jth: Crystal structure and biophysical properties of a complex between... -
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-Basic information
Entry | Database: PDB / ID: 1jth | ||||||
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Title | Crystal structure and biophysical properties of a complex between the N-terminal region of SNAP25 and the SNARE region of syntaxin 1a | ||||||
Components |
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Keywords | ENDOCYTOSIS/EXOCYTOSIS / coiled-coil / polar layer / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information BLOC-1 complex / myosin head/neck binding / 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 / positive regulation of norepinephrine secretion ...BLOC-1 complex / myosin head/neck binding / 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 / positive regulation of norepinephrine secretion / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / regulation of establishment of protein localization / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / 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 docking / chloride channel inhibitor activity / SNARE complex / SNAP receptor activity / secretion by cell / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / regulation of exocytosis / neurotransmitter secretion / positive regulation of hormone secretion / neurotransmitter receptor internalization / ATP-dependent protein binding / neurotransmitter transport / protein localization to membrane / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / insulin secretion / synaptic vesicle priming / Neutrophil degranulation / endosomal transport / regulation of synapse assembly / myosin binding / modulation of excitatory postsynaptic potential / regulation of neuron projection development / exocytosis / positive regulation of exocytosis / synaptic vesicle exocytosis / voltage-gated potassium channel activity / associative learning / positive regulation of excitatory postsynaptic potential / protein sumoylation / synaptic vesicle endocytosis / endomembrane system / calcium channel inhibitor activity / long-term memory / voltage-gated potassium channel complex / axonal growth cone / presynaptic active zone membrane / somatodendritic compartment / photoreceptor inner segment / axonogenesis / SNARE binding / acrosomal vesicle / locomotory behavior / filopodium / secretory granule / long-term synaptic potentiation / postsynaptic density membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / trans-Golgi network / positive regulation of insulin secretion / terminal bouton / neuron differentiation / synaptic vesicle membrane / kinase binding / calcium-dependent protein binding / protein-macromolecule adaptor activity / synaptic vesicle / actin cytoskeleton / presynapse / lamellipodium / presynaptic membrane / cell cortex / growth cone / postsynapse / nuclear membrane / transmembrane transporter binding / postsynaptic density / cytoskeleton Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Misura, K.M.S. / Gonzalez Jr., L.C. / May, A.P. / Scheller, R.H. / Weis, W.I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structure and biophysical properties of a complex between the N-terminal SNARE region of SNAP25 and syntaxin 1a. Authors: Misura, K.M. / Gonzalez Jr., L.C. / May, A.P. / Scheller, R.H. / Weis, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jth.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jth.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jth ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jth | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9525.569 Da / Num. of mol.: 2 / Fragment: N-terminal SNARE motif Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pQE9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60881 #2: Protein | Mass: 9102.500 Da / Num. of mol.: 2 / Fragment: H3, SNARE motif Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): JM190 / References: UniProt: P32851 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.5 Details: ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: BL9-2 / Wavelength: 0.9292, 0.9795, 0.9797, 1.005 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 11, 2001 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. all: 20657 / Num. obs: 18147 / % possible obs: 87.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.02 / Net I/σ(I): 24 | |||||||||||||||
Reflection shell | Resolution: 2→30 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.6 / % possible all: 98.8 | |||||||||||||||
Reflection | *PLUS % possible obs: 96.8 % / Redundancy: 2.4 % | |||||||||||||||
Reflection shell | *PLUS % possible obs: 98.8 % / Redundancy: 2.3 % |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 549679.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.652 Å2 / ksol: 0.37228 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 12.2 % / Rfactor obs: 0.265 / Rfactor Rfree: 0.284 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 52.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.367 / % reflection Rfree: 12.8 % / Rfactor Rwork: 0.355 |