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Yorodumi- PDB-5ccg: Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long u... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ccg | ||||||
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Title | Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) | ||||||
Components |
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Keywords | ENDOCYTOSIS / EXOCYTOSIS / XFEL structure / synaptic fusion complex / Synaptotagmin1 / neuronal SNARE 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 / 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 ...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 / 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 / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / spontaneous neurotransmitter secretion / 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 / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / regulation of synaptic vesicle priming / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulated exocytosis / calcium ion sensor activity / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / regulation of establishment of protein localization / storage vacuole / regulation of calcium ion-dependent exocytosis / 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 / exocytic vesicle / 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 / regulation of exocytosis / 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 / positive regulation of hormone secretion / neurotransmitter secretion / neurotransmitter receptor internalization / calcium-dependent phospholipid binding / ATP-dependent protein binding / protein localization to membrane / neuron projection terminus / presynaptic cytosol / 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 synaptic vesicle exocytosis / regulation of synapse assembly / postsynaptic cytosol / low-density lipoprotein particle receptor binding / clathrin binding / myosin binding / regulation of dopamine secretion / regulation of neuron projection development / phosphatidylserine binding / exocytosis / voltage-gated potassium channel activity / positive regulation of exocytosis / presynaptic active zone / synaptic vesicle exocytosis / modulation of excitatory postsynaptic potential Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Zhou, Q. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Weis, W.I. / Brunger, A.T. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. ...Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. / Lemke, H.T. / Pfuetzner, R.A. / Choi, U.B. / Weis, W.I. / Diao, J. / 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 | 5ccg.cif.gz | 275.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ccg.ent.gz | 219.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ccg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ccg_validation.pdf.gz | 478.7 KB | Display | wwPDB validaton report |
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Full document | 5ccg_full_validation.pdf.gz | 495.5 KB | Display | |
Data in XML | 5ccg_validation.xml.gz | 47.6 KB | Display | |
Data in CIF | 5ccg_validation.cif.gz | 64.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/5ccg ftp://data.pdbj.org/pub/pdb/validation_reports/cc/5ccg | HTTPS FTP |
-Related structure data
Related structure data | 5cchC 5cciC 5ccjC 1n7sS 1uowS 3f04S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Authors state that the biological assembly includes Chain A, B, C, D, Chain E 273-421, Chain F 273-421, Chain F 141-265 from symmetric neighbor. |
-Components
-Protein , 3 types, 7 molecules AGBHEFK
#1: Protein | Mass: 7231.061 Da / Num. of mol.: 2 / Fragment: UNP residues 28-89 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2, Syb2 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63045 #2: Protein | Mass: 7837.957 Da / Num. of mol.: 2 / Fragment: UNP residues 191-256 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32851 #5: Protein | Mass: 32247.197 Da / Num. of mol.: 3 / Fragment: UNP residues 141-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707 |
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-Synaptosomal-associated protein ... , 2 types, 4 molecules CIDJ
#3: Protein | Mass: 9030.114 Da / Num. of mol.: 2 / Fragment: UNP residues 7-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60881 #4: Protein | Mass: 7471.368 Da / Num. of mol.: 2 / Fragment: UNP residues 141-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60881 |
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-Non-polymers , 2 types, 37 molecules
#6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 72 |
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-Sample preparation
Crystal | Density Matthews: 5.56 Å3/Da / Density % sol: 77.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.3 Å |
Detector | Type: RAYONIX MX-325 / Detector: CCD / Date: May 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→20 Å / Num. obs: 39174 / % possible obs: 87.6 % / Redundancy: 5 % / CC1/2: 0.927 / Rmerge(I) obs: 0.397 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.5→3.62 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.355 / % possible all: 65.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N7S,3F04,1UOW Resolution: 3.5→19.972 Å / SU ML: 0.88 / Cross valid method: FREE R-VALUE / σ(F): 1.84 / Phase error: 38.85 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→19.972 Å
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Refine LS restraints |
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LS refinement shell |
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