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- PDB-1sf1: NMR STRUCTURE OF HUMAN INSULIN under Amyloidogenic Condition, 15 ... -

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Basic information

Entry
Database: PDB / ID: 1sf1
TitleNMR STRUCTURE OF HUMAN INSULIN under Amyloidogenic Condition, 15 STRUCTURES
Components
  • INSULIN A CHAIN
  • Insulin
KeywordsHORMONE/GROWTH FACTOR / HORMONE / HUMAN INSULIN / HORMONE-GROWTH FACTOR COMPLEX
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 feeding behavior / negative regulation of fatty acid metabolic process ...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 feeding behavior / negative regulation of fatty acid metabolic process / 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 / negative regulation of reactive oxygen species biosynthetic process / positive regulation of cellular protein metabolic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / Regulation of insulin secretion / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / regulation of cellular amino acid metabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / fatty acid homeostasis / endosome lumen / transport vesicle / positive regulation of insulin receptor signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / negative regulation of acute inflammatory response / regulation of transmembrane transporter activity / positive regulation of cell differentiation / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / regulation of synaptic plasticity / positive regulation of brown fat cell differentiation / cognition / regulation of protein localization / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / vasodilation / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / insulin receptor signaling pathway / glucose metabolic process / Golgi lumen / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of MAPK cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell migration / positive regulation of protein kinase B signaling / Amyloid fiber formation / Golgi membrane / G protein-coupled receptor signaling pathway / amyloid fibril formation / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin-like superfamily / Insulin family signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsWeiss, M.A. / Hua, Q.X.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Mechanism of insulin fibrillation: the structure of insulin under amyloidogenic conditions resembles a protein-folding intermediate
Authors: Hua, Q.X. / Weiss, M.A.
History
DepositionFeb 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INSULIN A CHAIN
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,8182
Polymers5,8182
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin /


Mass: 3433.953 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121NOESY
131COSY
1413D 15N-separated NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR AND 15N-3D HETERONUCLEAR NMR TECHNIQUES.

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Sample preparation

DetailsContents: 0.5 mM 15N-labeled sample / Solvent system: pH 2.4 and 60C, 90% H2O/10%D2O
Sample conditionspH: 2.4 / Pressure: ambient / Temperature: 333 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 INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR2.1BRUNGERrefinement
VNMR 6.1B6.1BVarianstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: RMSD VALUES FOR ALL 15 STRUCTURES VERSUS GEOMETRIC AVERAGE: (BACKBONE, A2-A20, B4-B24) 2.27 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: 15

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