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- PDB-2jsh: obestatin NMR structure in SDS/DPC micellar solution -

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Basic information

Entry
Database: PDB / ID: 2jsh
Titleobestatin NMR structure in SDS/DPC micellar solution
ComponentsAppetite-regulating hormone, Obestatin
KeywordsHORMONE / Obestatin / micellar solution / DPC / SDS / Alternative splicing / Amidation / Lipoprotein / Secreted
Function / homology
Function and homology information


positive regulation of response to food / positive regulation of gastro-intestinal system smooth muscle contraction / ghrelin receptor binding / negative regulation of locomotion / neuronal dense core vesicle lumen / positive regulation of bone development / positive regulation of gastric mucosal blood circulation / positive regulation of small intestinal transit / growth hormone-releasing hormone activity / negative regulation of circadian sleep/wake cycle, REM sleep ...positive regulation of response to food / positive regulation of gastro-intestinal system smooth muscle contraction / ghrelin receptor binding / negative regulation of locomotion / neuronal dense core vesicle lumen / positive regulation of bone development / positive regulation of gastric mucosal blood circulation / 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 / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of corticotropin secretion / positive regulation of cortisol secretion / gastric acid secretion / positive regulation of growth / positive regulation of feeding behavior / positive regulation of growth rate / positive regulation of eating behavior / positive regulation of small intestine smooth muscle contraction / positive regulation of appetite / G alpha (q) signalling events / adult feeding behavior / positive regulation of growth hormone secretion / actin polymerization or depolymerization / positive regulation of synapse assembly / positive regulation of vascular endothelial cell proliferation / negative regulation of interleukin-1 beta production / 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 / decidualization / negative regulation of tumor necrosis factor production / negative regulation of insulin secretion / response to electrical stimulus / synapse assembly / positive regulation of adipose tissue development / response to hormone / excitatory postsynaptic potential / G protein-coupled receptor binding / visual learning / positive regulation of insulin secretion / Schaffer collateral - CA1 synapse / hormone activity / negative regulation of inflammatory response / response to estrogen / positive regulation of cold-induced thermogenesis / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / postsynapse / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / axon / glutamatergic synapse / negative regulation of apoptotic process / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Preproghrelin peptide / Motilin/ghrelin-associated peptide / Motilin/ghrelin / Motilin/ghrelin-associated peptide / Motilin/ghrelin
Similarity search - Domain/homology
Appetite-regulating hormone
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsD'Ursi, A.M. / Scrima, M. / Esposito, C. / Campiglia, P.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Obestatin conformational features: a strategy to unveil obestatin's biological role?
Authors: Scrima, M. / Campiglia, P. / Esposito, C. / Gomez-Monterrey, I. / Novellino, E. / D'Ursi, A.M.
History
DepositionJul 5, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Appetite-regulating hormone, Obestatin


Theoretical massNumber of molelcules
Total (without water)2,5191
Polymers2,5191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)28 / 50target function
RepresentativeModel #1

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Components

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


Mass: 2518.827 Da / Num. of mol.: 1 / Fragment: residues 76-98 / Source method: obtained synthetically / Details: The peptides were chemical synthesized / References: UniProt: Q9EQX0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY

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Sample preparation

DetailsContents: 2.7 mM [U-100% 2H] SDS, 27 mM [U-100% 2H] DPC, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.7 mMSDS[U-100% 2H]1
27 mMDPC[U-100% 2H]1
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
DYANAGuntert, Braun and Wuthrichstructure solution
DYANAGuntert, Braun and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 28

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