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Yorodumi- PDB-5giw: Solution NMR structure of Humanin containing a D-isomerized serin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5giw | ||||||
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Title | Solution NMR structure of Humanin containing a D-isomerized serine residue | ||||||
Components | Humanin | ||||||
Keywords | APOPTOSIS / D-Ser / Alzheimer disease | ||||||
Function / homology | Function and homology information negative regulation of interleukin-18 production / receptor antagonist activity / negative regulation of neuroinflammatory response / negative regulation of interleukin-1 production / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of response to oxidative stress / negative regulation of execution phase of apoptosis / Formyl peptide receptors bind formyl peptides and many other ligands / negative regulation of amyloid fibril formation / leukocyte chemotaxis ...negative regulation of interleukin-18 production / receptor antagonist activity / negative regulation of neuroinflammatory response / negative regulation of interleukin-1 production / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of response to oxidative stress / negative regulation of execution phase of apoptosis / Formyl peptide receptors bind formyl peptides and many other ligands / negative regulation of amyloid fibril formation / leukocyte chemotaxis / sperm flagellum / supramolecular fiber organization / sperm midpiece / mitochondrion organization / G protein-coupled receptor binding / negative regulation of inflammatory response / cellular response to amyloid-beta / : / cell-cell signaling / G alpha (i) signalling events / G alpha (q) signalling events / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / signaling receptor binding / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular space / extracellular region / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Furuita, K. / Sugiki, T. / Alsanousi, N. / Fujiwara, T. / Kojima, C. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: Solution NMR structure and inhibitory effect against amyloid-beta fibrillation of Humanin containing a d-isomerized serine residue Authors: Alsanousi, N. / Sugiki, T. / Furuita, K. / So, M. / Lee, Y.H. / Fujiwara, T. / Kojima, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5giw.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5giw.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 5giw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/5giw ftp://data.pdbj.org/pub/pdb/validation_reports/gi/5giw | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2691.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IVG9 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 2.0 mM D-Ser-containing humanin, trifluoroethanol/water Details: peptides were dissolved in a 7:3 [v/v] H2O/TFE-d3 solution Label: sample_1 / Solvent system: trifluoroethanol/water |
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Sample | Conc.: 2.0 mM / Component: D-Ser-containing humanin / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: 0 Not defined / Label: conditions_1 / pH: 7 Not defined / Pressure: 1 bar / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |