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- PDB-2b4n: Solution Structure of Glucose-Dependent Insulinotropic Polypeptide -

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Basic information

Entry
Database: PDB / ID: 2b4n
TitleSolution Structure of Glucose-Dependent Insulinotropic Polypeptide
ComponentsGastric inhibitory polypeptide
KeywordsHORMONE/GROWTH FACTOR / GIP / MOLECULAR MODELLING / HELIX / DIABETES / OBESITY / HORMONE-GROWTH FACTOR COMPLEX
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 / endocrine pancreas development / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / response to selenium ion / positive regulation of D-glucose transmembrane transport / triglyceride homeostasis ...gastric inhibitory polypeptide receptor binding / digestive system development / gastric inhibitory peptide signaling pathway / glucagon receptor binding / regulation of fatty acid biosynthetic process / endocrine pancreas development / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / response to selenium ion / positive regulation of D-glucose transmembrane transport / triglyceride homeostasis / response to acidic pH / exploration behavior / response to lipid / response to starvation / positive regulation of cAMP/PKA signal transduction / response to amino acid / response to axon injury / response to glucose / sensory perception of pain / regulation of insulin secretion / adult locomotory behavior / female pregnancy / : / positive regulation of insulin secretion / hormone activity / memory / response to peptide hormone / long-term synaptic potentiation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / secretory granule lumen / G alpha (s) signalling events / endoplasmic reticulum lumen / response to xenobiotic stimulus / neuronal cell body / signal transduction / extracellular space / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #590 / Gastric inhibitory polypeptide / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Gastric inhibitory polypeptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, CONJUGATE-GRADIENT MINIMISATION, POWELL MINIMISATION
AuthorsAlana, I. / Hewage, C.M. / O'Harte, F.P.M. / Malthouse, J.P.G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: NMR and alanine scan studies of glucose-dependent insulinotropic polypeptide in water.
Authors: Alana, I. / Parker, J.C. / Gault, V.A. / Flatt, P.R. / O'harte, F.P. / Malthouse, J.P. / Hewage, C.M.
History
DepositionSep 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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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)20 / 200target function
RepresentativeModel #1lowest target function

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Components

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


Mass: 4990.586 Da / Num. of mol.: 1 / Fragment: residues 52-93 / Source method: isolated from a natural source / Source: (natural) 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
111DQF-COSY
1212D TOCSY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM GIP, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 3.3 / Pressure: AMBIENT / Temperature: 298 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 DRXBrukerDRX5001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX9003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5BRUKERcollection
XwinNMR3.5BRUKERprocessing
Sparky3.11GODDARD AND KNELLERdata analysis
CYANA1.0.6GUENTERTstructure solution
SYBYL6.81refinement
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, CONJUGATE-GRADIENT MINIMISATION, POWELL MINIMISATION
Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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