[English] 日本語
Yorodumi- PDB-5kj8: Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long u... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kj8 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction | ||||||
Components |
| ||||||
Keywords | ENDOCYTOSIS / EXOCYTOSIS / XFEL STRUCTURE / SYNAPTIC FUSION COMPLEX / SYNAPTOTAGMIN1 / NEURONAL SNARE COMPLEX | ||||||
Function / homology | Function and homology information : / : / negative regulation of secretion by cell / RHOF GTPase cycle / RHOB GTPase cycle / RHOD GTPase cycle / RHOG GTPase cycle / ER-Phagosome pathway / RAC2 GTPase cycle / RHOH GTPase cycle ...: / : / negative regulation of secretion by cell / RHOF GTPase cycle / RHOB GTPase cycle / RHOD GTPase cycle / RHOG GTPase cycle / ER-Phagosome pathway / RAC2 GTPase cycle / RHOH GTPase cycle / Retrograde transport at the Trans-Golgi-Network / RHOQ GTPase cycle / RAC1 GTPase cycle / BLOC-1 complex / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / RHOA GTPase cycle / 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 / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / 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 / regulated exocytosis / calcium ion sensor activity / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / regulation of establishment of protein localization / 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 / intracellular organelle / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / vesicle docking / intracellular vesicle / exocytic vesicle / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / positive regulation of dopamine secretion / protein heterooligomerization / clathrin-coated vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / 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 / retrograde transport, endosome to Golgi / 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 Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.1 Å | ||||||
Authors | Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zhou, Q. / Zhao, M. / Sauter, N.K. / Brewster, A.S. / Weis, W.I. / Brunger, A.T. | ||||||
Citation | Journal: Elife / Year: 2016 Title: Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. Authors: Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Zhou, Q. / Zhao, M. / Brewster, A.S. / Michels-Clark, T. / Holton, J.M. / Sauter, N.K. / Weis, W.I. / Brunger, A.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5kj8.cif.gz | 248.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5kj8.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kj8_validation.pdf.gz | 472.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5kj8_full_validation.pdf.gz | 484.6 KB | Display | |
Data in XML | 5kj8_validation.xml.gz | 46.6 KB | Display | |
Data in CIF | 5kj8_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/5kj8 ftp://data.pdbj.org/pub/pdb/validation_reports/kj/5kj8 | HTTPS FTP |
-Related structure data
Related structure data | 5kj7C 1n7sS 1uowS 3f04S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
-Protein , 3 types, 7 molecules AGBHEFK
#1: Protein | Mass: 7231.061 Da / Num. of mol.: 2 / Fragment: UNP residues 14-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp3, Syb3 / Production host: Escherichia coli (E. coli) / References: UniProt: P63025 #2: Protein | Mass: 7706.761 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P32851 #5: Protein | Mass: 31988.838 Da / Num. of mol.: 3 / Fragment: UNP residues 141-419 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, 4 molecules CIDJ
#3: Protein | Mass: 8741.725 Da / Num. of mol.: 2 / Fragment: UNP residues 9-83 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 #4: Protein | Mass: 7340.173 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P60881 |
---|
-Non-polymers , 1 types, 14 molecules
#6: Chemical | ChemComp-CA / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.3 Å3/Da / Density % sol: 76.78 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 4.1→50 Å / Num. obs: 27282 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 4.1→4.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.8 / % possible all: 99.1 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N7S, 3F04, 1UOW Resolution: 4.1→49.64 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.25
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 155 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.1→49.64 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|