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- PDB-6h3e: Receptor-bound Ghrelin conformation -

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Basic information

Entry
Database: PDB / ID: 6h3e
TitleReceptor-bound Ghrelin conformation
ComponentsAppetite-regulating hormone
KeywordsHORMONE / Neuropeptide / acyl chain / growth hormone secretagogue receptor / GPCR / lipopeptide hormone / obesity / diabetes / addiction.
Function / homology
Function and homology information


ghrelin receptor binding / positive regulation of bone development / positive regulation of gastric mucosal blood circulation / negative regulation of locomotion / cortisol secretion / positive regulation of small intestinal transit / growth hormone-releasing hormone activity / negative regulation of circadian sleep/wake cycle, REM sleep / positive regulation of circadian sleep/wake cycle, non-REM sleep / regulation of response to food ...ghrelin receptor binding / positive regulation of bone development / positive regulation of gastric mucosal blood circulation / negative regulation of locomotion / cortisol secretion / positive regulation of small intestinal transit / growth hormone-releasing hormone activity / negative regulation of circadian sleep/wake cycle, REM sleep / positive regulation of circadian sleep/wake cycle, non-REM sleep / regulation of response to food / regulation of gastric motility / regulation of transmission of nerve impulse / gastric acid secretion / positive regulation of corticotropin secretion / positive regulation of cortisol secretion / growth hormone secretion / positive regulation of growth rate / positive regulation of eating behavior / positive regulation of appetite / positive regulation of small intestine smooth muscle contraction / adult feeding behavior / positive regulation of growth hormone secretion / positive regulation of growth hormone receptor signaling pathway / positive regulation of multicellular organism growth / actin polymerization or depolymerization / positive regulation of synapse assembly / cartilage development / negative regulation of interleukin-1 beta production / positive regulation of vascular endothelial cell proliferation / regulation of postsynapse organization / postsynaptic modulation of chemical synaptic transmission / protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / dendrite development / negative regulation of endothelial cell proliferation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / decidualization / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of insulin secretion / response to electrical stimulus / synapse assembly / positive regulation of adipose tissue development / excitatory postsynaptic potential / hormone-mediated signaling pathway / negative regulation of angiogenesis / Peptide ligand-binding receptors / response to hormone / G protein-coupled receptor binding / Schaffer collateral - CA1 synapse / positive regulation of insulin secretion / negative regulation of inflammatory response / response to estrogen / glucose metabolic process / positive regulation of cold-induced thermogenesis / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / postsynapse / G alpha (q) signalling events / secretory granule lumen / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / axon / glutamatergic synapse / negative regulation of apoptotic process / extracellular space / extracellular region
Similarity search - Function
Preproghrelin peptide / Motilin/ghrelin-associated peptide / Motilin/ghrelin / Motilin/ghrelin-associated peptide / Motilin/ghrelin
Similarity search - Domain/homology
octan-1-amine / Appetite-regulating hormone
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsFerre, G. / Damian, M. / M'Kadmi, C. / Saurel, O. / Czaplicki, G. / Demange, P. / Marie, J. / Fehrentz, J.A. / Baneres, J.L. / Milon, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0011-03 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structure and dynamics of G protein-coupled receptor-bound ghrelin reveal the critical role of the octanoyl chain.
Authors: Ferre, G. / Louet, M. / Saurel, O. / Delort, B. / Czaplicki, G. / M'Kadmi, C. / Damian, M. / Renault, P. / Cantel, S. / Gavara, L. / Demange, P. / Marie, J. / Fehrentz, J.A. / Floquet, N. / ...Authors: Ferre, G. / Louet, M. / Saurel, O. / Delort, B. / Czaplicki, G. / M'Kadmi, C. / Damian, M. / Renault, P. / Cantel, S. / Gavara, L. / Demange, P. / Marie, J. / Fehrentz, J.A. / Floquet, N. / Milon, A. / Baneres, J.L.
History
DepositionJul 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Appetite-regulating hormone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2602
Polymers2,1301
Non-polymers1291
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, The peptide primary structure has been verified by mass spectrometry.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint0 kcal/mol
Surface area2140 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Appetite-regulating hormone / Growth hormone secretagogue / Growth hormone-releasing peptide / Motilin-related peptide / Protein M46


Mass: 2130.301 Da / Num. of mol.: 1 / Mutation: S3D / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBU3
#2: Chemical ChemComp-FKZ / octan-1-amine


Mass: 129.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19N

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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
161isotropic12D 1H-1H TOCSY
122isotropic12D 1H-1H NOESY
152isotropic12D 1H-1H TOCSY
133isotropic13D 1H-1H-15N NOESY-HMQC
173isotropic12D 1H-15N SOFAST-HMQC
144isotropic13D 1H-1H-15N NOESY-HMQC
184isotropic12D 1H-15N SOFAST-HMQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.37 mM [U-15N]-Phe-Leu-Val Ghrelin 1-18, 2.05 uM [U-2H] Ghrelin receptor, 90% H2O/10% D2OGhrelin receptor (growth hormone secretagogue receptor, GHSR) reconstituted in POPC/POPG 3/2 mol/mol nanodiscs.Ghrelin total binding for 1H1H-NOESY90% H2O/10% D2O
solution21.37 mM [U-15N]-Phe-Leu-Val Ghrelin 1-18, 2.05 uM [U-2H] Ghrelin receptor, 2.05 uM JMV5327, 90% H2O/10% D2OGhrelin receptor (growth hormone secretagogue receptor, GHSR) reconstituted in POPC/POPG 3/2 mol/mol nanodiscs.Ghrelin unspecific binding for 1H1H-NOESY90% H2O/10% D2O
solution31.15 mM [U-15N]-Phe-Leu-Val-Ser-Gln-Glu Ghrelin 1-18, 1.72 uM [U-2H] Ghrelin receptor, 90% H2O/10% D2OGhrelin receptor (growth hormone secretagogue receptor, GHSR) reconstituted in POPC/POPG 3/2 mol/mol nanodiscs.Ghrelin total binding for 1H1H15N-NOESY-HMQC90% H2O/10% D2O
solution41.15 mM [U-15N]-Phe-Leu-Val-Ser-Gln-Glu Ghrelin 1-18, 1.72 uM [U-2H] Ghrelin receptor, 1.72 uM JMV5327, 90% H2O/10% D2OGhrelin receptor (growth hormone secretagogue receptor, GHSR) reconstituted in POPC/POPG 3/2 mol/mol nanodiscs.Ghrelin unspecific binding for 1H1H15N-NOESY-HMQC90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.37 mMGhrelin 1-18[U-15N]-Phe-Leu-Val1
2.05 uMGhrelin receptor[U-2H]1
1.37 mMGhrelin 1-18[U-15N]-Phe-Leu-Val2
2.05 uMGhrelin receptor[U-2H]2
2.05 uMJMV5327natural abundance2
1.15 mMGhrelin 1-18[U-15N]-Phe-Leu-Val-Ser-Gln-Glu3
1.72 uMGhrelin receptor[U-2H]3
1.15 mMGhrelin 1-18[U-15N]-Phe-Leu-Val-Ser-Gln-Glu4
1.72 uMGhrelin receptor[U-2H]4
1.72 uMJMV5327natural abundance4
Sample conditionsDetails: The buffer is 20mM [U-2H]-MES pH 6.5, 100mM KCl, 100uM DSS, 10%vol D2O.
Ionic strength: 100 KCl mM / Label: Conditions for all samples / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 280 K / Temperature err: 1

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
Sparky1.2T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Franciscopeak picking
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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