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- PDB-2mpi: Solution structure of B24G insulin -

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Basic information

Entry
Database: PDB / ID: 2mpi
TitleSolution structure of B24G insulin
Components
  • insulin chain A
  • insulin chain B
KeywordsPROTEIN BINDING / insulin structure / insulin mutant
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of acute inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / COPI-mediated anterograde transport / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / Regulation of insulin secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / positive regulation of nitric oxide mediated signal transduction / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / transport vesicle / neuron projection maintenance / endosome lumen / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of cell differentiation / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of brown fat cell differentiation / regulation of synaptic plasticity / regulation of transmembrane transporter activity / positive regulation of long-term synaptic potentiation / cognition / regulation of protein localization / activation of protein kinase B activity / positive regulation of cytokine production / positive regulation of glucose import / acute-phase response / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor signaling pathway / insulin receptor binding / positive regulation of protein localization to nucleus / vasodilation / Golgi lumen / glucose metabolic process / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of MAPK cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of protein kinase B signaling / positive regulation of NF-kappaB transcription factor activity / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / regulation of transcription, DNA-templated / endoplasmic reticulum lumen / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsYang, Y. / Wickramasinghe, N.P. / Hua, Q. / Weiss, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Protective hinge in insulin opens to enable its receptor engagement.
Authors: Menting, J.G. / Yang, Y. / Chan, S.J. / Phillips, N.B. / Smith, B.J. / Whittaker, J. / Wickramasinghe, N.P. / Whittaker, L.J. / Pandyarajan, V. / Wan, Z.L. / Yadav, S.P. / Carroll, J.M. / ...Authors: Menting, J.G. / Yang, Y. / Chan, S.J. / Phillips, N.B. / Smith, B.J. / Whittaker, J. / Wickramasinghe, N.P. / Whittaker, L.J. / Pandyarajan, V. / Wan, Z.L. / Yadav, S.P. / Carroll, J.M. / Strokes, N. / Roberts, C.T. / Ismail-Beigi, F. / Milewski, W. / Steiner, D.F. / Chauhan, V.S. / Ward, C.W. / Weiss, M.A. / Lawrence, M.C.
History
DepositionMay 19, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: insulin chain A
B: insulin chain B


Theoretical massNumber of molelcules
Total (without water)5,7042
Polymers5,7042
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide insulin chain A


Mass: 2383.698 Da / Num. of mol.: 1 / Mutation: K53P P52K F48G H34D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide insulin chain B


Mass: 3320.772 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution structure of B24G insulin
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1222D 1H-1H TOCSY
1312D DQF-COSY
1422D DQF-COSY
1512D 1H-1H NOESY
1622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM protein, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.3 mMentity-11
0.3 mMentity-22
Sample conditionsIonic strength: 0.5 / pH: 8 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance7001
Bruker AvanceBrukerAvance7002

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Processing

NMR software
NameDeveloperClassification
InsightIIAccelrys Software Inc.structure solution
X-PLORBrungerrefinement
xwinnmrBruker Biospincollection
VNMRVariandata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
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: 18

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