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- PDB-2gd3: NMR structure of S14G-humanin in 30% TFE solution -

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Basic information

Entry
Database: PDB / ID: 2gd3
TitleNMR structure of S14G-humanin in 30% TFE solution
ComponentsHumanin
KeywordsUNKNOWN FUNCTION / S14G-Humanin / Humanin / Alzheimer's disease / Neuroprotection / NMR / CD
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 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
Humanin family / Humanin family
Similarity search - Domain/homology
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsBenaki, D. / Zikos, C. / Evangelou, A. / Livaniou, E. / Vlassi, M. / Mikros, E. / Pelecanou, M.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2006
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: Journal: Biochem.Biophys.Res.Commun. / Year: 2005
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: Journal: Biochem.Biophys.Res.Commun. / Year: 2001
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
DepositionMar 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Humanin


Theoretical massNumber of molelcules
Total (without water)2,6611
Polymers2,6611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 30014 convergent conformers are presented having the lowest energy and the best structural quality in Ramachadran plot
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Humanin


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
2312D NOESY
2412D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 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
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
160 microM NaN3 2.7 ambient 298 K
260 microM NaN3 2.7 ambient 280 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
Sparky3Goddard, T.D. & Kneller, D.G.data analysis
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer 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

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