+Open data
-Basic information
Entry | Database: PDB / ID: 5vfe | ||||||
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Title | Synaptotagmin 1 C2A domain, lead-bound | ||||||
Components | Synaptotagmin-1 | ||||||
Keywords | METAL BINDING PROTEIN / C2A DOMAIN | ||||||
Function / homology | Function and homology information GABA synthesis, release, reuptake and degradation / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Glutamate 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 ...GABA synthesis, release, reuptake and degradation / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Glutamate 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 / dense core granule / positive regulation of vesicle fusion / chromaffin granule membrane / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / vesicle docking / positive regulation of calcium ion-dependent exocytosis / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of dopamine secretion / protein heterooligomerization / Clathrin-mediated endocytosis / 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 / 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Taylor, A.B. / Hart, P.J. / Igumenova, T.I. | ||||||
Citation | Journal: Metallomics / Year: 2018 Title: High affinity interactions of Pb2+with synaptotagmin I. Authors: Katti, S. / Her, B. / Srivastava, A.K. / Taylor, A.B. / Lockless, S.W. / Igumenova, T.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vfe.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vfe.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vfe_validation.pdf.gz | 438.8 KB | Display | wwPDB validaton report |
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Full document | 5vfe_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 5vfe_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 5vfe_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/5vfe ftp://data.pdbj.org/pub/pdb/validation_reports/vf/5vfe | HTTPS FTP |
-Related structure data
Related structure data | 5vffC 5vfgC 3f00S 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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-Components
#1: Protein | Mass: 14525.588 Da / Num. of mol.: 2 / Fragment: residues 140-265 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syt1 / Plasmid: PET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46096 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris pH 5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→40.55 Å / Num. obs: 53772 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 13.6 Å2 / Rpim(I) all: 0.022 / Rsym value: 0.064 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.38→1.45 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7848 / Rpim(I) all: 0.317 / Rsym value: 0.61 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F00 Resolution: 1.38→29.988 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 16.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→29.988 Å
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Refine LS restraints |
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LS refinement shell |
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