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Yorodumi- PDB-1ugk: Solution structure of the first C2 domain of synaptotagmin IV fro... -
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-Basic information
Entry | Database: PDB / ID: 1ugk | ||||||
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Title | Solution structure of the first C2 domain of synaptotagmin IV from human fetal brain (KIAA1342) | ||||||
Components | Synaptotagmin IV | ||||||
Keywords | PROTEIN BINDING / BETA SANDWICH / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information : / negative regulation of short-term neuronal synaptic plasticity / vesicle fusion with vesicle / secretory granule maturation / negative regulation of dense core granule exocytosis / positive regulation of dense core granule exocytosis / negative regulation of retrograde trans-synaptic signaling by neuropeptide / dense core granule membrane / negative regulation of catecholamine secretion / negative regulation of vesicle fusion ...: / negative regulation of short-term neuronal synaptic plasticity / vesicle fusion with vesicle / secretory granule maturation / negative regulation of dense core granule exocytosis / positive regulation of dense core granule exocytosis / negative regulation of retrograde trans-synaptic signaling by neuropeptide / dense core granule membrane / negative regulation of catecholamine secretion / negative regulation of vesicle fusion / : / : / microvesicle / syntaxin-3 binding / dense core granule cytoskeletal transport / regulation of calcium ion-dependent exocytosis / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / exocytic vesicle / negative regulation of calcium ion-dependent exocytosis / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / positive regulation of dendrite extension / neurotransmitter secretion / astrocyte projection / calcium-dependent phospholipid binding / neuron projection terminus / positive regulation of glutamate secretion / syntaxin-1 binding / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / neuronal dense core vesicle / regulation of endocytosis / negative regulation of protein secretion / vesicle-mediated transport / cellular response to calcium ion / SNARE binding / brain development / memory / neuron projection / protein heterodimerization activity / axon / intracellular membrane-bounded organelle / neuronal cell body / synapse / dendrite / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Nagashima, T. / Hayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. ...Nagashima, T. / Hayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Ohara, O. / Nagase, T. / Kikuno, R. / Nakayama, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the first C2 domain of synaptotagmin IV from human fetal brain (KIAA1342) Authors: Nagashima, T. / Hayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / ...Authors: Nagashima, T. / Hayashi, F. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Ohara, O. / Nagase, T. / Kikuno, R. / Nakayama, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ugk.cif.gz | 846.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ugk.ent.gz | 705.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ugk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ugk_validation.pdf.gz | 346.1 KB | Display | wwPDB validaton report |
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Full document | 1ugk_full_validation.pdf.gz | 536.7 KB | Display | |
Data in XML | 1ugk_validation.xml.gz | 69.2 KB | Display | |
Data in CIF | 1ugk_validation.cif.gz | 85.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/1ugk ftp://data.pdbj.org/pub/pdb/validation_reports/ug/1ugk | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15519.801 Da / Num. of mol.: 1 / Fragment: C2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: Kazusa cDNA fj00418 / Plasmid: P020924-36 / References: UniProt: Q9H2B2 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.75mM 13C, 15N-labeled protein; 20mM Tris-d11; 100mM NaCl; 1mM DTT; 0.1mM NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.1 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |