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Yorodumi- PDB-5w5c: Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C... -
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-Basic information
Entry | Database: PDB / ID: 5w5c | ||||||
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Title | Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex | ||||||
Components |
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Keywords | EXOCYTOSIS / Prefusion primed complex / Neuronal Exocytosis / Synaptotagmin / SNARE complex / Complexin / synchronous neurotransmitter release | ||||||
Function / homology | Function and homology information regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane / regulation of 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 / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding ...regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane / regulation of 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 / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / calcium-dependent activation of synaptic vesicle fusion / calcium ion sensor activity / regulation of regulated secretory pathway / extrinsic component of presynaptic 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 / spontaneous neurotransmitter secretion / Lysosome Vesicle Biogenesis / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / 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 / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / chromaffin granule membrane / 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 / eosinophil degranulation / vesicle fusion / regulation of calcium ion-dependent exocytosis / vesicle docking / neurotransmitter transmembrane transporter activity / positive regulation of calcium ion-dependent exocytosis / exocytic vesicle / regulation of neurotransmitter secretion / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / positive regulation of dendrite extension / Golgi to plasma membrane protein transport / regulation of exocytosis / positive regulation of hormone secretion / neurotransmitter secretion / neurotransmitter receptor internalization / protein localization to membrane / calcium-dependent phospholipid binding / ATP-dependent protein binding / neuron projection terminus / neurotransmitter transport / regulation of synaptic vesicle recycling / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / clathrin-coated vesicle / synaptic vesicle priming / Neutrophil degranulation / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / regulation of synaptic vesicle exocytosis / low-density lipoprotein particle receptor binding / clathrin binding / myosin binding / regulation of dopamine secretion / exocytosis / phosphatidylserine binding / voltage-gated potassium channel activity / synaptic vesicle exocytosis / positive regulation of exocytosis Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Zhou, Q. / Brunger, A.T. | ||||||
Citation | Journal: Nature / Year: 2017 Title: The primed SNARE-complexin-synaptotagmin complex for neuronal exocytosis. Authors: Zhou, Q. / Zhou, P. / Wang, A.L. / Wu, D. / Zhao, M. / Sudhof, T.C. / 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 | 5w5c.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w5c.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 5w5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w5c_validation.pdf.gz | 493.5 KB | Display | wwPDB validaton report |
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Full document | 5w5c_full_validation.pdf.gz | 511 KB | Display | |
Data in XML | 5w5c_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 5w5c_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/5w5c ftp://data.pdbj.org/pub/pdb/validation_reports/w5/5w5c | HTTPS FTP |
-Related structure data
Related structure data | 5w5dC 1kilS 1uowS 3f04S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 4704.220 Da / Num. of mol.: 1 / Fragment: UNP residues 29-66 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2, Syb2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63045 |
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-Protein , 3 types, 3 molecules BEF
#2: Protein | Mass: 7837.957 Da / Num. of mol.: 1 / Fragment: UNP residues 191-256 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851 |
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#5: Protein | Mass: 9612.908 Da / Num. of mol.: 1 / Fragment: UNP residues 1-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cplx1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63041 |
#6: Protein | Mass: 32376.311 Da / Num. of mol.: 1 / Fragment: UNP residues 140-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21707 |
-Synaptosomal-associated protein ... , 2 types, 2 molecules CD
#3: Protein | Mass: 9030.114 Da / Num. of mol.: 1 / Fragment: UNP residues 7-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881 |
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#4: Protein | Mass: 7471.368 Da / Num. of mol.: 1 / Fragment: UNP residues 141-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881 |
-Non-polymers , 3 types, 285 molecules
#7: Chemical | ChemComp-MG / | ||
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#8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 100 mM HEPES, pH7.4, 15-20% PEG3350, 200 mM ammonium formate PH range: 6.8-7.8 |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97922 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.85→64.126 Å / Num. obs: 61236 / % possible obs: 99.8 % / Redundancy: 17.8 % / Biso Wilson estimate: 41.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.024 / Rrim(I) all: 0.102 / Net I/σ(I): 19.4 / Num. measured all: 1087199 / Scaling rejects: 0 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KIL, 3F04, 1UOW Resolution: 1.85→64.126 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 188.65 Å2 / Biso mean: 76.1997 Å2 / Biso min: 26.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→64.126 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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