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- PDB-2m5q: Solution structure of lipidated glucagon analog in d-TFE -

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Basic information

Entry
Database: PDB / ID: 2m5q
TitleSolution structure of lipidated glucagon analog in d-TFE
ComponentsGlucagon
KeywordsLIPID BINDING PROTEIN / GLUCAGON / DIABETES / OBESITY / LIPIDATED
Function / homology
Function and homology information


glucagon receptor binding / : / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / cellular response to glucagon stimulus / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis ...glucagon receptor binding / : / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / cellular response to glucagon stimulus / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / protein kinase A signaling / positive regulation of peptidyl-threonine phosphorylation / response to activity / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / 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
GAMMA-L-GLUTAMIC ACID / PALMITIC ACID / Pro-glucagon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWard, B.P. / Ma, D.
CitationJournal: To be Published
Title: Structural Changes Associated with Peptide Lipidation Broaden Biological Function
Authors: Ward, B.P. / Ottaway, N.L. / Ma, D. / Gelfanov, V.M. / Giedroc, D.P. / Perez-Tilve, D.P. / Tschop, M.H. / Dimarchi, R.D.
History
DepositionMar 4, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Glucagon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9984
Polymers3,4471
Non-polymers5513
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Glucagon /


Mass: 3446.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275
#2: Chemical ChemComp-GGL / GAMMA-L-GLUTAMIC ACID / L-GLUTAMIC ACID / Glutamic acid


Type: L-gamma-peptide, C-delta linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 0.7 mM protein, 95% [U-100% 2H] TFE/5% H2O / Solvent system: 95% [U-100% 2H] TFE/5% H2O
SampleConc.: 0.7 mM / Component: protein-1
Sample conditionsIonic strength: 0 / pH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Field strength: 600 MHz

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Processing

NMR softwareName: XPLOR-NIH / Developer: BRUNGER / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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