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- PDB-1plx: NMR structure of Methionine-Enkephalin in fast tumbling Bicelles/DMPG -

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Basic information

Entry
Database: PDB / ID: 1plx
TitleNMR structure of Methionine-Enkephalin in fast tumbling Bicelles/DMPG
ComponentsMet-enkephalin 1
KeywordsNEUROPEPTIDE
Function / homology
Function and homology information


synaptic vesicle lumen / neuronal dense core vesicle lumen / chromaffin granule lumen / opioid receptor binding / opioid peptide activity / synaptic signaling via neuropeptide / general adaptation syndrome, behavioral process / aggressive behavior / positive regulation of behavioral fear response / symmetric synapse ...synaptic vesicle lumen / neuronal dense core vesicle lumen / chromaffin granule lumen / opioid receptor binding / opioid peptide activity / synaptic signaling via neuropeptide / general adaptation syndrome, behavioral process / aggressive behavior / positive regulation of behavioral fear response / symmetric synapse / G protein-coupled opioid receptor signaling pathway / response to epinephrine / cell body fiber / sensory perception / cellular response to vitamin D / neuropeptide hormone activity / startle response / transmission of nerve impulse / locomotory exploration behavior / response to immobilization stress / behavioral fear response / neuropeptide signaling pathway / glial cell proliferation / axon terminus / cellular response to cAMP / sensory perception of pain / cellular response to transforming growth factor beta stimulus / Peptide ligand-binding receptors / Post-translational protein phosphorylation / response to nicotine / response to toxic substance / cellular response to virus / response to calcium ion / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / response to estradiol / cellular response to oxidative stress / G alpha (i) signalling events / chemical synaptic transmission / perikaryon / response to ethanol / response to lipopolysaccharide / response to hypoxia / endoplasmic reticulum lumen / neuronal cell body / dendrite / signal transduction / extracellular region / plasma membrane
Similarity search - Function
Proenkephalin A / Opioid neuropeptide precursor / Vertebrate endogenous opioids neuropeptide / Endogenous opioids neuropeptides precursors signature.
Similarity search - Domain/homology
MethodSOLUTION NMR / simulated annealing
AuthorsMarcotte, I. / Separovic, F. / Auger, M. / Gagne, S.M.
CitationJournal: Biophys.J. / Year: 2004
Title: A multidimensional (1)h NMR investigation of the conformation of methionine-enkephalin in fast-tumbling bicelles.
Authors: Marcotte, I. / Separovic, F. / Auger, M. / Gagne, S.M.
History
DepositionJun 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Met-enkephalin 1


Theoretical massNumber of molelcules
Total (without water)5741
Polymers5741
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)80 / 200structures with the lowest energy
RepresentativeModel #11 and 2, closest to the average of each of the two conformers

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Components

#1: Protein/peptide Met-enkephalin 1


Mass: 573.662 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPETIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN)
References: UniProt: P01210

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121g-COSY
NMR detailsText: PFG diffusion experiments were also performed on the sample

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Sample preparation

DetailsContents: 5.1uM Menk; (DMPC+DMPG)/DHPC: 0.5:1 (molar ratio); DMPC/DMPG: 9:1 (molar ratio); Lipid/peptide: 25:1 (molar ratio); 10% w/v of lipids in water; 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 9mM / pH: 4.8 / Pressure: ambient / Temperature: 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
NMRPipe2.0 Rev 2001.117.12.48Frank Delaglioprocessing
NMRView5.0.4Bruce A. Johnsondata analysis
CNS1.1Axel T. Brungerstructure solution
CNS1.1Axel T. Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2 phi angle and 58 NOE-derived distance constraints. 1000 high-temperature steps were used (15 ps) up to a final temperature of 50000 K then 1000 ...Details: The structures are based on a total of 2 phi angle and 58 NOE-derived distance constraints. 1000 high-temperature steps were used (15 ps) up to a final temperature of 50000 K then 1000 cooling steps (250 K, 15 ps) were applied. Finally, 10 cycles of 200 minimization steps were performed A repel constant value of 0.8 was used
NMR representativeSelection criteria: 1 and 2, closest to the average of each of the two conformers
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 80

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