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- PDB-1nau: NMR Solution Structure of the Glucagon Antagonist [desHis1, desPh... -

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Basic information

Entry
Database: PDB / ID: 1nau
TitleNMR Solution Structure of the Glucagon Antagonist [desHis1, desPhe6, Glu9]Glucagon Amide in the Presence of Perdeuterated Dodecylphosphocholine Micelles
ComponentsGlucagon
KeywordsHORMONE/GROWTH FACTOR / HELIX / TURN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


glucagon receptor binding / negative regulation of execution phase of apoptosis / feeding behavior / : / cellular response to glucagon stimulus / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / protein kinase A signaling ...glucagon receptor binding / negative regulation of execution phase of apoptosis / feeding behavior / : / cellular response to glucagon stimulus / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / protein kinase A signaling / positive regulation of gluconeogenesis / response to activity / positive regulation of peptidyl-threonine phosphorylation / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / hormone activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / glucose homeostasis / positive regulation of peptidyl-serine phosphorylation / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Glucagon / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry, restrained molecular dynamics
Model type detailsminimized average
AuthorsYing, J. / Ahn, J.-M. / Jacobsen, N.E. / Brown, M.F. / Hruby, V.J.
CitationJournal: Biochemistry / Year: 2003
Title: NMR Solution Structure of the Glucagon Antagonist [desHis1, desPhe6, Glu9]Glucagon Amide in the Presence of Perdeuterated Dodecylphosphocholine Micelles
Authors: Ying, J. / Ahn, J.-M. / Jacobsen, N.E. / Brown, M.F. / Hruby, V.J.
History
DepositionNov 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucagon


Theoretical massNumber of molelcules
Total (without water)3,2131
Polymers3,2131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 5015 structures with the lowest restraint energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Glucagon / / Glicentin-related polypeptide (GRPP)


Mass: 3213.495 Da / Num. of mol.: 1 / Mutation: DEL(H53), DEL(F58), D7E / Source method: obtained synthetically
Details: This sequence was chemically synthesized. It was obtained by modifying the sequence of glucagon, which occurs naturally in Homo sapiens (human).
References: UniProt: P01275

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 7mM [desHis1, desPhe6, Glu9]Glucagon Amide; 50 mM sodium phosphate buffer; 283 mM dodecylphosphocholine-d38 micelles; 1 mM sodium azide; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM sodium phosphate; 1mM sodium azide / pH: 6.0 / Pressure: ambient / Temperature: 310 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: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMRBrukercollection
Felix2000Accelrysprocessing
Felix2000Accelrysdata analysis
DGIIwithin InsightII 2000Accelrysstructure solution
Discoverwithin InsightII 2000Accelrysrefinement
RefinementMethod: distance geometry, restrained molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 486 restraints, 475 are NOE-derived distance restraints, 11 dihedral angle restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: 15 structures with the lowest restraint energy
Conformers calculated total number: 50 / Conformers submitted total number: 16

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