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- PDB-1wso: The solution structures of human Orexin-A -

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Basic information

Entry
Database: PDB / ID: 1wso
TitleThe solution structures of human Orexin-A
ComponentsOrexin-A
KeywordsNEUROPEPTIDE / Hypocretin / Orexin / GPCR / Orphan G-protein coupled receptor / Narcolepsy
Function / homology
Function and homology information


type 1 orexin receptor binding / type 2 orexin receptor binding / negative regulation of transmission of nerve impulse / Orexin and neuropeptides FF and QRFP bind to their respective receptors / positive regulation of transmission of nerve impulse / regulation of neurotransmitter secretion / neuropeptide hormone activity / positive regulation of calcium ion transport / sleep / : ...type 1 orexin receptor binding / type 2 orexin receptor binding / negative regulation of transmission of nerve impulse / Orexin and neuropeptides FF and QRFP bind to their respective receptors / positive regulation of transmission of nerve impulse / regulation of neurotransmitter secretion / neuropeptide hormone activity / positive regulation of calcium ion transport / sleep / : / eating behavior / temperature homeostasis / negative regulation of DNA replication / response to starvation / negative regulation of potassium ion transport / neuropeptide signaling pathway / rough endoplasmic reticulum / excitatory postsynaptic potential / secretory granule / positive regulation of cold-induced thermogenesis / synaptic vesicle / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / chemical synaptic transmission / postsynapse / perinuclear region of cytoplasm / extracellular region
Similarity search - Function
Prepro-orexin / Prepro-orexin
Similarity search - Domain/homology
Hypocretin neuropeptide precursor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsIkegami, T. / Takai, T.
CitationJournal: J.Pept.Sci. / Year: 2006
Title: Orexin-A is composed of a highly conserved C-terminal and a specific, hydrophilic N-terminal region, revealing the structural basis of specific recognition by the orexin-1 receptor
Authors: Takai, T. / Takaya, T. / Nakano, M. / Akutsu, H. / Nakagawa, A. / Aimoto, S. / Nagai, K. / Ikegami, T.
History
DepositionNov 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Source and taxonomy
Category: entity_poly / pdbx_entity_src_syn ...entity_poly / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.details ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orexin-A


Theoretical massNumber of molelcules
Total (without water)3,5691
Polymers3,5691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Orexin-A / Hypocretin-1


Mass: 3569.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43612

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
1422D TOCSY
1522D NOESY
16115N-1H-HSQC
17113C-1H-HSQC
NMR detailsText: The structures were determined using 2D homonuclear and 15N, 13C natural abundance heteronuclear experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.76mM orexin-A; 18mM potassium phosphate buffer90% H2O/10% D2O
20.76mM orexin-A; 18mM potassium phosphate buffer99.9% D20
Sample conditionsIonic strength: 18mM potassium phosphate / pH: 6 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglio, F.processing
Sparky3.106Goddard, T. D.data analysis
CYANA1.0.6Guentert, P.structure solution
TALOS2003.027.13.05Delaglio, F.data analysis
CYANA1.0.6Guentert, P.refinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
Details: The N- and C-termini are modified with Pyrrolidone carboxylic acid, or pyroglutamic acid, and an amide group, respectively. Two intra-molecular disulfide bonds are formed between Cys6 and ...Details: The N- and C-termini are modified with Pyrrolidone carboxylic acid, or pyroglutamic acid, and an amide group, respectively. Two intra-molecular disulfide bonds are formed between Cys6 and Cys12, and between Cys7 and Cys14.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 30

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