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- PDB-8c5h: NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytoso... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c5h | ||||||
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Title | NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytosolic domain of Synaptotagmin-1 | ||||||
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![]() | METAL BINDING PROTEIN / Nanobody / Synaptotagmin 1 | ||||||
Function / homology | ![]() regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / calcium ion-regulated exocytosis of neurotransmitter / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / Glutamate Neurotransmitter Release Cycle ...regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / calcium ion-regulated exocytosis of neurotransmitter / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / calcium-dependent activation of synaptic vesicle fusion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / dense core granule / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / positive regulation of calcium ion-dependent exocytosis / vesicle docking / exocytic vesicle / vesicle organization / protein heterooligomerization / vesicle fusion / positive regulation of dopamine secretion / calcium-ion regulated exocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of dendrite extension / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / syntaxin binding / syntaxin-1 binding / clathrin binding / low-density lipoprotein particle receptor binding / regulation of synaptic vesicle exocytosis / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle exocytosis / presynaptic active zone / postsynaptic cytosol / excitatory synapse / detection of calcium ion / positive regulation of synaptic transmission / presynaptic cytosol / regulation of synaptic transmission, glutamatergic / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / SNARE binding / hippocampal mossy fiber to CA3 synapse / secretory granule / molecular condensate scaffold activity / terminal bouton / phospholipid binding / response to calcium ion / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / postsynaptic membrane / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein heterodimerization activity / axon / lipid binding / calcium ion binding / glutamatergic synapse / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martinez-Carranza, M. / Stenmark, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging And Low Linkage-Error in Super-Resolution Microscopy. Authors: Queiroz Zetune Villa Real, K. / Mougios, N. / Rehm, R. / Sograte-Idrissi, S. / Albert, L. / Rahimi, A.M. / Maidorn, M. / Hentze, J. / Martinez-Carranza, M. / Hosseini, H. / Saal, K.A. / ...Authors: Queiroz Zetune Villa Real, K. / Mougios, N. / Rehm, R. / Sograte-Idrissi, S. / Albert, L. / Rahimi, A.M. / Maidorn, M. / Hentze, J. / Martinez-Carranza, M. / Hosseini, H. / Saal, K.A. / Oleksiievets, N. / Prigge, M. / Tsukanov, R. / Stenmark, P. / Fornasiero, E.F. / Opazo, F. | ||||||
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 KB | Display | ![]() |
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PDB format | ![]() | 88.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443 KB | Display | ![]() |
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Full document | ![]() | 444.4 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5t0rS ![]() 6i2gS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 15365.521 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Antibody | Mass: 13537.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A51 anti rat synaptotagmin-1 nanobody / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
#3: Chemical | ChemComp-CA / | ||||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 M Di-Malic acid pH 7.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→46.9 Å / Num. obs: 49689 / % possible obs: 97.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 31.06 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.85 |
Reflection shell | Resolution: 1.68→1.71 Å / Rmerge(I) obs: 3.822 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 1246 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5T0R, 6I2G Resolution: 1.68→41.26 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.67 / 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: 1.68→41.26 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 2.8137 Å / Origin y: 9.3993 Å / Origin z: 8.6404 Å
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Refinement TLS group | Selection details: all |