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- PDB-2jmn: NMR structure of human insulin mutant His-B10-Asp, Pro-B28-Lys, L... -

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Entry
Database: PDB / ID: 2jmn
TitleNMR structure of human insulin mutant His-B10-Asp, Pro-B28-Lys, Lys-B29-Pro, 20 structures
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE/GROWTH FACTOR / HORMONE / HUMAN INSULIN / MUTANT / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Synthesis, secretion, and deacylation of Ghrelin / Signaling by Insulin receptor / Regulation of insulin secretion / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / IRS activation / Signal attenuation / Insulin receptor signalling cascade / COPI-mediated anterograde transport / Regulation of gene expression in beta cells / Insulin processing ...Synthesis, secretion, and deacylation of Ghrelin / Signaling by Insulin receptor / Regulation of insulin secretion / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / IRS activation / Signal attenuation / Insulin receptor signalling cascade / COPI-mediated anterograde transport / Regulation of gene expression in beta cells / Insulin processing / Amyloid fiber formation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Insulin receptor recycling / negative regulation of glycogen catabolic process / alpha-beta T cell activation / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / negative regulation of NAD(P)H oxidase activity / positive regulation of respiratory burst / regulation of protein secretion / positive regulation of peptide hormone secretion / negative regulation of respiratory burst involved in inflammatory response / negative regulation of blood vessel diameter / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of lipid biosynthetic process / regulation of transmembrane transporter activity / positive regulation of dendritic spine maintenance / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of lipid catabolic process / negative regulation of protein secretion / negative regulation of protein oligomerization / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / regulation of cellular amino acid metabolic process / positive regulation of glycolytic process / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / endosome lumen / regulation of synaptic plasticity / positive regulation of insulin receptor signaling pathway / cognition / neuron projection maintenance / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / positive regulation of cytokine secretion / positive regulation of mitotic nuclear division / negative regulation of acute inflammatory response / regulation of protein localization / positive regulation of cell differentiation / positive regulation of long-term synaptic potentiation / activation of protein kinase B activity / positive regulation of glucose import / positive regulation of blood vessel diameter / hormone activity / negative regulation of protein catabolic process / acute-phase response / negative regulation of proteolysis / insulin receptor signaling pathway / positive regulation of protein localization to nucleus / insulin receptor binding / positive regulation of nitric-oxide synthase activity / glucose metabolic process / cell-cell signaling / Golgi lumen / wound healing / glucose homeostasis / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / protease binding / positive regulation of cell migration / positive regulation of protein kinase B signaling / Golgi membrane / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / cellular protein metabolic process / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Insulin / Insulin-like / Insulin family / Insulin, conserved site / Insulin/IGF/Relaxin family / Insulin-like superfamily / Insulin family signature.
Insulin
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
Model detailsDKP-insulin mutant HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO
AuthorsHua, Q.X. / Hu, S.Q. / Frank, B.H. / Jia, W.H. / Chu, Y.C. / Wang, S.H. / Burke, G.T. / Katsoyannis, P.G. / Weiss, M.A.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Mapping the functional surface of insulin by design: structure and function of a novel A-chain analogue.
Authors: Hua, Q.X. / Hu, S.Q. / Frank, B.H. / Jia, W. / Chu, Y.C. / Wang, S.H. / Burke, G.T. / Katsoyannis, P.G. / Weiss, M.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 21, 2006 / Release: Dec 5, 2006
RevisionDateData content typeGroupProviderType
1.0Dec 5, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)5,7952
Polymers5,7952
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3410.894 Da / Num. of mol.: 1 / Mutation: H10D, P28K, K29P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P01308

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: DKP-insulin mutant HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO
NMR experiment

Conditions-ID: 1 / Solution-ID: 1

Experiment-IDType
12D TOCSY
2NOESY
3COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 0.7 mM INSULIN, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: INSULIN
Sample conditionspH: 7.0 / 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 DRXBrukerDRX8001
VARIAN INOVAVarianINOVA7002
VARIAN INOVAVarianINOVA603

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarianstructure solution
X-PLOR3.85Brungerstructure solution
X-PLOR3.85Brungerrefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: RMSD VALUES FOR ALL 20 STRUCTURES VERSUS GEOMETRIC AVERAGE: (BACKBONE, A2-A20, B4-B24) 0.26 ANGSTROM
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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