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Open data
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Basic information
Entry | Database: PDB / ID: 2gd3 | ||||||
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Title | NMR structure of S14G-humanin in 30% TFE solution | ||||||
![]() | Humanin | ||||||
![]() | UNKNOWN FUNCTION / S14G-Humanin / Humanin / Alzheimer's disease / Neuroprotection / NMR / CD | ||||||
Function / homology | ![]() 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 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 response to oxidative stress ...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 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 response to oxidative stress / 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 | ||||||
Method | SOLUTION NMR / simulated annealing torsion angle dynamics | ||||||
![]() | Benaki, D. / Zikos, C. / Evangelou, A. / Livaniou, E. / Vlassi, M. / Mikros, E. / Pelecanou, M. | ||||||
![]() | ![]() Title: Solution structure of Ser14Gly-humanin, a potent rescue factor against neuronal cell death in Alzheimer's disease. Authors: Benaki, D. / Zikos, C. / Evangelou, A. / Livaniou, E. / Vlassi, M. / Mikros, E. / Pelecanou, M. #1: ![]() Title: Solution structure of humanin, a peptide against Alzheimer's disease-related neurotoxicity. Authors: Benaki, D. / Zikos, C. / Evangelou, A. / Livaniou, E. / Vlassi, M. / Mikros, E. / Pelecanou, M. #2: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2001 Title: A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer's disease genes and Abeta. Authors: Hashimoto, Y. / Niikura, T. / Tajima, H. / Yasukawa, T. / Sudo, H. / Ito, Y. / Kita, Y. / Kawasumi, M. / Kouyama, K. / Doyu, M. / Sobue, G. / Koide, T. / Tsuji, S. / Lang, J. / Kurokawa, K. / Nishimoto, I. #3: ![]() Title: Mechanisms of Neuroprotection by a Novel Rescue Factor Humanin from Swedish Mutant Amyloid Precursor Protein Authors: Hashimoto, Y. / Ito, Y. / Niikura, T. / Shao, Z. / Hata, M. / Oyama, F. / Nishimoto, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.1 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 342 KB | Display | ![]() |
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Full document | ![]() | 411.4 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 2661.239 Da / Num. of mol.: 1 / Mutation: S14G / Source method: obtained synthetically Details: S14G-humanin was prepared by Fmoc-solid phase synthesis on o-Cl-trityl-amidomethyl polystyrene resin (Evangelou, A., Zikos, C., Livaniou, E., Evangelatos, G.P. "Highyield, solid-phase ...Details: S14G-humanin was prepared by Fmoc-solid phase synthesis on o-Cl-trityl-amidomethyl polystyrene resin (Evangelou, A., Zikos, C., Livaniou, E., Evangelatos, G.P. "Highyield, solid-phase synthesis of humanin, an Alzheimer's disease associated, novel 24-mer peptide which contains a difficult sequence" J. Peptide Sci. 2004, 10, 631 635). The peptide was purified to 95% with semi-preparative RP-HPLC and suitably characterized. The sequence is naturally found in 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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NMR details | Text: This structure was determined using standard 2D homonuclear techniques |
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Sample preparation
Details | Contents: 1.3 mM S14G-humanin; 60 microM NaN3 to prevent microbial growth; H2O/TFE-d3 7:3; pH 2.6 (uncorrected for the presence of TFE); at 298 and 280 K Solvent system: H2O/TFE-d3 7:3 | |||||||||||||||
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing torsion angle dynamics / Software ordinal: 1 Details: Starting from an extended structure a total of 300 structures were generated from 133 NOE-derived distance restraints and 2 distance restraints based on temperature coefficient data using ...Details: Starting from an extended structure a total of 300 structures were generated from 133 NOE-derived distance restraints and 2 distance restraints based on temperature coefficient data using the simulated annealing and energy minimization protocol in the program CNS, version 1.1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: 14 convergent conformers are presented having the lowest energy and the best structural quality in Ramachadran plot Conformers calculated total number: 300 / Conformers submitted total number: 14 |