+Open data
-Basic information
Entry | Database: PDB / ID: 1uov | ||||||
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Title | Calcium binding domain C2B | ||||||
Components | SYNAPTOTAGMIN I | ||||||
Keywords | GLYCOPROTEIN / TRANSMEMBRANE / SYNAPSE / LIPOPROTEIN | ||||||
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 / 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 | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Cheng, Y. / Sequeira, S.M. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uov.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uov.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1uov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uov_validation.pdf.gz | 315.2 KB | Display | wwPDB validaton report |
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Full document | 1uov_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 1uov_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1uov_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/1uov ftp://data.pdbj.org/pub/pdb/validation_reports/uo/1uov | HTTPS FTP |
-Related structure data
Related structure data | 1tjmC 1tjxC 1uowC 1k5wS 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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Unit cell |
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-Components
#1: Protein | Mass: 17822.727 Da / Num. of mol.: 1 / Fragment: C2B DOMAIN, RESIDUES 271-421 Source method: isolated from a genetically manipulated source Details: 3 CALCIUM IONS BOUND / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707 | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | pH: 5 / Details: pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS / Wavelength: 1.5418 |
Detector | Date: May 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. obs: 22306 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 24.18 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 4.13 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K5W Resolution: 1.65→20 Å / SU B: 1.262 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 15.327 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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