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- PDB-7s3o: NMR Solution Structure of hGal(2-12)KK, a solubility-tagged trunc... -

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Basic information

Entry
Database: PDB / ID: 7s3o
TitleNMR Solution Structure of hGal(2-12)KK, a solubility-tagged truncation of the human neuropeptide galanin
ComponentsGalanin
KeywordsNEUROPEPTIDE / binding epitope / synthetic peptide
Function / homology
Function and homology information


galanin receptor binding / type 1 galanin receptor binding / type 2 galanin receptor binding / type 3 galanin receptor binding / galanin receptor activity / positive regulation of large conductance calcium-activated potassium channel activity / positive regulation of timing of catagen / positive regulation of cortisol secretion / regulation of glucocorticoid metabolic process / negative regulation of lymphocyte proliferation ...galanin receptor binding / type 1 galanin receptor binding / type 2 galanin receptor binding / type 3 galanin receptor binding / galanin receptor activity / positive regulation of large conductance calcium-activated potassium channel activity / positive regulation of timing of catagen / positive regulation of cortisol secretion / regulation of glucocorticoid metabolic process / negative regulation of lymphocyte proliferation / protein kinase A signaling / neuropeptide hormone activity / feeding behavior / insulin secretion / response to immobilization stress / neuropeptide signaling pathway / Peptide ligand-binding receptors / secretory granule / response to insulin / response to estrogen / G alpha (i) signalling events / positive regulation of apoptotic process / response to xenobiotic stimulus / neuronal cell body / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Galanin / Galanin precursor / Galanin message associated peptide (GMAP) / Galanin / Galanin message associated peptide (GMAP) / Galanin signature. / Galanin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKraichely, K.N. / Clinkscales, S.E. / Parnham, S. / Giuliano, M.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103499-20 United States
CitationJournal: Biochemistry / Year: 2022
Title: Minimal Increments of Hydrophobic Collapse within the N-Terminus of the Neuropeptide Galanin.
Authors: Kraichely, K.N. / Clinkscales, S.E. / Hendy, C.M. / Mendoza, E.A. / Parnham, S. / Giuliano, M.W.
History
DepositionSep 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galanin


Theoretical massNumber of molelcules
Total (without water)1,4511
Polymers1,4511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Peptide state was determined to be monomeric after observation of no dispersion, broadening, or loss of resolution in peaks in its 1D 1H NMR spectrum over a 50- ...Evidence: assay for oligomerization, Peptide state was determined to be monomeric after observation of no dispersion, broadening, or loss of resolution in peaks in its 1D 1H NMR spectrum over a 50-fold range of concentration from 0.1 mM up to 5 mM.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Galanin


Mass: 1450.705 Da / Num. of mol.: 1 / Mutation: P45K, H46K / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P22466
Has protein modificationY

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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 COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H ROESY
141isotropic11D 1H acquisition

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Sample preparation

DetailsType: solution
Contents: 5 mM hGal(2-12)KK, 4.14 mM D3 sodium acetate, 5.86 mM D4 acetic acid, 95% H2O/5% D2O
Details: 5 mM hGal(2-12)KK peptide 10 mM deuterated (d3/d4) sodium acetate/acetic acid buffer pH 4.6
Label: SEC-I-072A / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMhGal(2-12)KKnatural abundance1
4.14 mMsodium acetateD31
5.86 mMacetic acidD41
Sample conditionsDetails: 5 mM hGal(2-12)KK peptide 10 mM deuterated (d3/d4) sodium acetate/acetic acid buffer pH 4.6
Ionic strength: 4.14 mM sodium acetate-d3 mM / Label: 1 / pH: 4.6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 400 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CNSBrunger A. T. et.al.structure calculation
MestreLab (Mnova / MestReNova / MestReC)MestreLab (Mnova / MestReNova / MestReC)chemical shift assignment
MestreLab (Mnova / MestReNova / MestReC)MestreLab (Mnova / MestReNova / MestReC)peak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 25

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