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- PDB-6k59: Structure of Glargine insulin in 20% acetic acid-d4 (pH 1.9) -

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Basic information

Entry
Database: PDB / ID: 6k59
TitleStructure of Glargine insulin in 20% acetic acid-d4 (pH 1.9)
Components
  • Glargine Insulin Chain-A
  • Glargine insulin Chain-B
KeywordsHORMONE / diabetes / insulin
Function / homology
Function and homology information


: / negative regulation of glycogen catabolic process / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / negative regulation of feeding behavior / negative regulation of acute inflammatory response ...: / negative regulation of glycogen catabolic process / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / negative regulation of feeding behavior / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / positive regulation of respiratory burst / alpha-beta T cell activation / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of dendritic spine maintenance / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of insulin receptor signaling pathway / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / nitric oxide-cGMP-mediated signaling / regulation of protein localization to plasma membrane / transport vesicle / Insulin receptor recycling / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / positive regulation of mitotic nuclear division / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of D-glucose import across plasma membrane / endosome lumen / positive regulation of protein secretion / acute-phase response / positive regulation of cytokine production / insulin receptor binding / wound healing / positive regulation of long-term synaptic potentiation / positive regulation of cell differentiation / positive regulation of neuron projection development / negative regulation of protein catabolic process / Regulation of insulin secretion / hormone activity / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of synaptic plasticity / vasodilation / Golgi lumen / cognition / glucose homeostasis / insulin receptor signaling pathway / regulation of protein localization / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / receptor ligand activity / negative regulation of gene expression / Golgi membrane / positive regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / : / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsRatha, B.N. / Kar, R.K. / Bhunia, A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research02(0292)/17/EMR-II India
CitationJournal: J.Phys.Chem.B / Year: 2020
Title: Molecular Details of a Salt Bridge and Its Role in Insulin Fibrillation by NMR and Raman Spectroscopic Analysis.
Authors: Ratha, B.N. / Kar, R.K. / Bednarikova, Z. / Gazova, Z. / Kotler, S.A. / Raha, S. / De, S. / Maiti, N.C. / Bhunia, A.
History
DepositionMay 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glargine Insulin Chain-A
B: Glargine insulin Chain-B


Theoretical massNumber of molelcules
Total (without water)6,0752
Polymers6,0752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, THE ZINC FREE FORM IS PREDOMINANTLY MONOMER IN 20% ACETIC ACID PH 1.9
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1600 Å2
ΔGint-16 kcal/mol
Surface area3500 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Glargine Insulin Chain-A


Mass: 2326.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P01308*PLUS
#2: Protein/peptide Glargine insulin Chain-B


Mass: 3748.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P01308*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 350 uM UNLABELLED PEPTIDE CHAIN A, 350 uM UNLABELLED PEPTIDE CHAIN B, 20% acetic acid/d4
Details: 2mg/ml Zn free glargine insulin in 20% acetic acid/d4 at pH 1.9
Label: GI / Solvent system: 20% acetic acid/d4
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
350 uMPEPTIDE CHAIN AUNLABELLED1
350 uMPEPTIDE CHAIN BUNLABELLED1
Sample conditionsDetails: 2mg/ml Zn free glargine insulin in 20% acetic acid/d4 at pH 1.9
Ionic strength: 0 mM / Label: GI_20% / pH: 1.9 pD / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: IIT KGP

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Processing

NMR software
NameVersionDeveloperClassification
Sparky12.1https://www.cgl.ucsf.edu/home/sparky/chemical shift assignment
TopSpinBruker Biospincollection
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Sparkyhttps://www.cgl.ucsf.edu/home/sparky/peak picking
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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