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- PDB-1tjx: Crystallographic Identification of Ca2+ Coordination Sites in Syn... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tjx | ||||||
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Title | Crystallographic Identification of Ca2+ Coordination Sites in Synaptotagmin I C2B Domain | ||||||
![]() | similar to synaptotagminI/p65 | ||||||
![]() | ENDOCYTOSIS/EXOCYTOSIS / Synaptotagmin I / C2B domain / Calcium binding / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | ![]() 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 / calcium ion sensor activity / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine 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 / calcium ion sensor activity / 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-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / vesicle docking / positive regulation of calcium ion-dependent exocytosis / 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 / syntaxin-1 binding / syntaxin binding / regulation of synaptic vesicle exocytosis / low-density lipoprotein particle receptor binding / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / synaptic vesicle exocytosis / excitatory synapse / synaptic vesicle endocytosis / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / cellular response to calcium ion / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / SNARE binding / secretory granule / terminal bouton / phospholipid binding / synaptic vesicle membrane / response to calcium ion / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cheng, Y. / Sequeira, S.M. / Malinina, L. / Tereshko, V. / Sollner, T.H. / Patel, D.J. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.9 KB | Display | ![]() |
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PDB format | ![]() | 93.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456 KB | Display | ![]() |
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Full document | ![]() | 458.5 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tjmC ![]() 1uovC ![]() 1uowC ![]() 1k5wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 1.04→19.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.04→1.07 Å / Total num. of bins used: 20 /
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