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- PDB-2m1e: Biosynthetic engineered B28K-B29P human insulin monomer structure... -

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Basic information

Entry
Database: PDB / ID: 2m1e
TitleBiosynthetic engineered B28K-B29P human insulin monomer structure in in water solutions.
Components(Insulin) x 2
KeywordsHORMONE / Human Insulin
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / 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 ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / 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 / regulation of cellular amino acid metabolic process / 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 / COPI-mediated anterograde transport / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / regulation of protein localization to plasma membrane / Regulation of insulin secretion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of cell differentiation / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of mitotic nuclear division / positive regulation of brown fat cell differentiation / regulation of synaptic plasticity / cognition / positive regulation of long-term synaptic potentiation / regulation of protein localization / positive regulation of cytokine production / activation of protein kinase B activity / 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 NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / 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/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin-like / Insulin-like superfamily / Insulin family signature. / Insulin, conserved site
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing
Model detailsfewest violations, model 1
AuthorsBocian, W. / Kozerski, L.
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: Biosynthetic engineered B28(K)-B29(P) human insulin monomer structure in water and in water/acetonitrile solutions.
Authors: Borowicz, P. / Bocian, W. / Sitkowski, J. / Bednarek, E. / Mikiewicz-Sygula, D. / Kurzynoga, D. / Stadnik, D. / Surmacz-Chwedoruk, W. / Kozminski, W. / Kozerski, L.
History
DepositionNov 26, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,8182
Polymers5,8182
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)20 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Insulin / / Insulin B chain / 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 / References: UniProt: P01308
#2: Protein/peptide Insulin / / Insulin B chain / Insulin A chain


Mass: 3433.953 Da / Num. of mol.: 1 / Mutation: P28K, K29P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / References: UniProt: P01308

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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
1322D 1H-1H NOESY
1422D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 - 3.0 mM insulin, residues 90-110, 2.5 - 3.0 mM insulin, residues 25-54, 90% H2O/10% D2O90% H2O/10% D2O
22.5 - 3.0 mM insulin, residues 90-110, 2.5 - 3.0 mM insulin, residues 25-54, 100% D2O100% D2O
Sample
UnitsComponentConc. range (mg/ml)Solution-ID
mMentity_1-12.5-3.01
mMentity_2-22.5-3.01
mMentity_1-32.5-3.02
mMentity_2-42.5-3.02
Sample conditionsIonic strength: 1 / pH: 2.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AMBER11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
AMBER11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
VNMRJ2.2 CVariancollection
SPARKY2.6Goddardchemical shift assignment
RefinementMethod: torsion angle dynamics, DGSA-distance geometry simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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