+Open data
-Basic information
Entry | Database: PDB / ID: 6lcy | ||||||
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Title | Crystal structure of Synaptotagmin-7 C2B in complex with IP6 | ||||||
Components | Synaptotagmin-7 | ||||||
Keywords | EXOCYTOSIS / Synaptotagmin-7 / IP6 / Insulin secretion | ||||||
Function / homology | Function and homology information calcium ion regulated lysosome exocytosis / vesicle-mediated cholesterol transport / regulation of glucagon secretion / synaptic vesicle recycling / phagosome-lysosome fusion / calcium-dependent activation of synaptic vesicle fusion / short-term synaptic potentiation / regulation of bone remodeling / dense core granule / calcium ion-regulated exocytosis of neurotransmitter ...calcium ion regulated lysosome exocytosis / vesicle-mediated cholesterol transport / regulation of glucagon secretion / synaptic vesicle recycling / phagosome-lysosome fusion / calcium-dependent activation of synaptic vesicle fusion / short-term synaptic potentiation / regulation of bone remodeling / dense core granule / calcium ion-regulated exocytosis of neurotransmitter / vesicle fusion / regulation of calcium ion-dependent exocytosis / positive regulation of calcium ion-dependent exocytosis / calcium-ion regulated exocytosis / plasma membrane repair / regulation of phagocytosis / early phagosome / calcium-dependent phospholipid binding / peroxisomal membrane / regulation of synaptic vesicle endocytosis / syntaxin binding / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / regulation of insulin secretion / GABA-ergic synapse / phagocytosis / axon terminus / cellular response to calcium ion / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / SNARE binding / synaptic vesicle membrane / phagocytic vesicle membrane / peroxisome / synaptic vesicle / presynaptic membrane / lysosome / calmodulin binding / lysosomal membrane / axon / neuronal cell body / glutamatergic synapse / synapse / calcium ion binding / dendrite / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å | ||||||
Authors | Zhang, Y. / Zhang, X. / Rao, F. / Wang, C. | ||||||
Citation | Journal: Nat Metab / Year: 2021 Title: 5-IP 7 is a GPCR messenger mediating neural control of synaptotagmin-dependent insulin exocytosis and glucose homeostasis. Authors: Zhang, X. / Li, N. / Zhang, J. / Zhang, Y. / Yang, X. / Luo, Y. / Zhang, B. / Xu, Z. / Zhu, Z. / Yang, X. / Yan, Y. / Lin, B. / Wang, S. / Chen, D. / Ye, C. / Ding, Y. / Lou, M. / Wu, Q. / ...Authors: Zhang, X. / Li, N. / Zhang, J. / Zhang, Y. / Yang, X. / Luo, Y. / Zhang, B. / Xu, Z. / Zhu, Z. / Yang, X. / Yan, Y. / Lin, B. / Wang, S. / Chen, D. / Ye, C. / Ding, Y. / Lou, M. / Wu, Q. / Hou, Z. / Zhang, K. / Liang, Z. / Wei, A. / Wang, B. / Wang, C. / Jiang, N. / Zhang, W. / Xiao, G. / Ma, C. / Ren, Y. / Qi, X. / Han, W. / Wang, C. / Rao, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lcy.cif.gz | 49 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lcy.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lcy_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6lcy_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6lcy_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 6lcy_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/6lcy ftp://data.pdbj.org/pub/pdb/validation_reports/lc/6lcy | HTTPS FTP |
-Related structure data
Related structure data | 3n5aS 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: 16455.207 Da / Num. of mol.: 1 / Fragment: C2B domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syt7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R0N7 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.11 Å3/Da / Density % sol: 75.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100mM NaCl, 50mM Tris-Cl, 1mM EDTA, 1mM DDT, 5mM IP6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 14840 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 30.64 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.043 / Rrim(I) all: 0.09 / Χ2: 0.847 / Net I/σ(I): 10.3 / Num. measured all: 60777 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N5A Resolution: 2.301→45.209 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.21 / 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 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.88 Å2 / Biso mean: 33.0726 Å2 / Biso min: 13.93 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.301→45.209 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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