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- PDB-5giw: Solution NMR structure of Humanin containing a D-isomerized serin... -

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Basic information

Entry
Database: PDB / ID: 5giw
TitleSolution NMR structure of Humanin containing a D-isomerized serine residue
ComponentsHumanin
KeywordsAPOPTOSIS / D-Ser / Alzheimer disease
Function / homology
Function and homology information


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 / 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 / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFuruita, K. / Sugiki, T. / Alsanousi, N. / Fujiwara, T. / Kojima, C.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: 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
DepositionJun 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: citation / database_2 ...citation / database_2 / entity / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Humanin


Theoretical massNumber of molelcules
Total (without water)2,6911
Polymers2,6911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2570 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Humanin / / Humanin mitochondrial / HNM


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: 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
SampleConc.: 2.0 mM / Component: D-Ser-containing humanin / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 7 Not defined / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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