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- PDB-2l70: NMR solution structure of GIP in micellular media -

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Basic information

Entry
Database: PDB / ID: 2l70
TitleNMR solution structure of GIP in micellular media
ComponentsGastric inhibitory polypeptide
KeywordsHORMONE / GIP / Docking / Ala-scan / Type 2 diabetes
Function / homology
Function and homology information


gastric inhibitory polypeptide receptor binding / digestive system development / gastric inhibitory peptide signaling pathway / glucagon receptor binding / regulation of fatty acid biosynthetic process / positive regulation of cAMP-mediated signaling / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / endocrine pancreas development / response to selenium ion / response to acidic pH ...gastric inhibitory polypeptide receptor binding / digestive system development / gastric inhibitory peptide signaling pathway / glucagon receptor binding / regulation of fatty acid biosynthetic process / positive regulation of cAMP-mediated signaling / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / endocrine pancreas development / response to selenium ion / response to acidic pH / positive regulation of glucose transmembrane transport / triglyceride homeostasis / exploration behavior / response to lipid / response to starvation / regulation of insulin secretion / response to axon injury / response to amino acid / response to glucose / sensory perception of pain / adult locomotory behavior / female pregnancy / long-term synaptic potentiation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / response to organic cyclic compound / hormone activity / memory / response to peptide hormone / Glucagon-type ligand receptors / G alpha (s) signalling events / secretory granule lumen / response to xenobiotic stimulus / endoplasmic reticulum lumen / neuronal cell body / signal transduction / extracellular space / extracellular region
Similarity search - Function
Gastric inhibitory polypeptide / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
Gastric inhibitory polypeptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsVenneti, K.C. / Alana, I. / O'Harte, F.P.M. / Malthouse, P.J.G. / Hewage, C.M.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Conformational, receptor interaction and alanine scan studies of glucose-dependent insulinotropic polypeptide
Authors: Venneti, K.C. / Malthouse, J.P.G. / O'Harte, F.P.M. / Hewage, C.M.
History
DepositionDec 1, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gastric inhibitory polypeptide


Theoretical massNumber of molelcules
Total (without water)4,9911
Polymers4,9911
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)15 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Gastric inhibitory polypeptide / GIP / Glucose-dependent insulinotropic polypeptide


Mass: 4990.586 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthesized on a peptide synthesizer using standard solid-phase Fmoc procedure
Source: (synth.) Homo sapiens (human) / References: UniProt: P09681

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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
1312D DQF-COSY

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Sample preparation

DetailsContents: 150mM DHPC; 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 150 mM / Component: DHPC-1
Sample conditionspH: 3.9 / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX9003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 15 / Representative conformer: 1

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