[English] 日本語
Yorodumi- PDB-1tjx: Crystallographic Identification of Ca2+ Coordination Sites in Syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tjx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystallographic Identification of Ca2+ Coordination Sites in Synaptotagmin I C2B Domain | ||||||
Components | similar to synaptotagminI/p65 | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / Synaptotagmin I / C2B domain / Calcium binding / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle ...synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / 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 / calcium ion sensor activity / regulation of calcium ion-dependent exocytosis / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle docking / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / calcium-ion regulated exocytosis / positive regulation of dendrite extension / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / presynaptic cytosol / syntaxin binding / syntaxin-1 binding / regulation of synaptic vesicle exocytosis / postsynaptic cytosol / low-density lipoprotein particle receptor binding / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / presynaptic active zone / synaptic vesicle exocytosis / synaptic vesicle endocytosis / excitatory synapse / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / hippocampal mossy fiber to CA3 synapse / SNARE binding / secretory granule / response to calcium ion / terminal bouton / phospholipid binding / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / postsynaptic membrane / cell differentiation / calmodulin binding / postsynaptic density / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||
Authors | Cheng, Y. / Sequeira, S.M. / Malinina, L. / Tereshko, V. / Sollner, T.H. / Patel, D.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Crystallographic identification of Ca2+ and Sr2+ coordination sites in synaptotagmin I C2B domain. Authors: Cheng, Y. / Sequeira, S.M. / Malinina, L. / Tereshko, V. / Sollner, T.H. / Patel, D.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1tjx.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1tjx.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tjx_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1tjx_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 1tjx_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1tjx_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tjx ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tjx | HTTPS FTP |
-Related structure data
Related structure data | 1tjmC 1uovC 1uowC 1k5wS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17822.727 Da / Num. of mol.: 1 / Fragment: C2B domain, residues 296-446 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21707 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
---|---|
Crystal grow | Temperature: 277 K / pH: 5 Details: ammonium sulfate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→20 Å / Num. obs: 85544 / % possible obs: 99 % / Redundancy: 5.55 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.04→1.06 Å / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.62 / % possible all: 96.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K5W Resolution: 1.04→19.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.335 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.29 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→19.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.04→1.07 Å / Total num. of bins used: 20 /
|