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- PDB-1aiy: R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 10 STRUCTURES -

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Entry
Database: PDB / ID: 1aiy
TitleR6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 10 STRUCTURES
Components(R6 INSULIN HEXAMER) x 2
KeywordsHORMONE / GLUCOSE METABOLISM
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 / negative regulation of reactive oxygen species biosynthetic process / negative regulation of lipid catabolic process / positive regulation of cellular protein metabolic 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 / positive regulation of glycolytic process / regulation of protein localization to plasma membrane / regulation of cellular amino acid metabolic process / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / endosome lumen / regulation of synaptic plasticity / cognition / positive regulation of protein autophosphorylation / neuron projection maintenance / positive regulation of insulin receptor signaling pathway / 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 / activation of protein kinase B activity / positive regulation of long-term synaptic potentiation / positive regulation of glucose import / positive regulation of blood vessel diameter / negative regulation of protein catabolic process / hormone activity / 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 / Golgi lumen / wound healing / cell-cell signaling / 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 / protease binding / positive regulation of NF-kappaB transcription factor activity / 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, ENERGY MINIMIZATION
AuthorsChang, X. / Jorgensen, A.M.M. / Bardrum, P. / Led, J.J.
CitationJournal: Biochemistry / Year: 1997
Title: Solution structures of the R6 human insulin hexamer.
Authors: Chang, X. / Jorgensen, A.M. / Bardrum, P. / Led, J.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 30, 1997 / Release: Nov 12, 1997
RevisionDateData content typeGroupProviderType
1.0Nov 12, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R6 INSULIN HEXAMER
B: R6 INSULIN HEXAMER
C: R6 INSULIN HEXAMER
D: R6 INSULIN HEXAMER
E: R6 INSULIN HEXAMER
F: R6 INSULIN HEXAMER
G: R6 INSULIN HEXAMER
H: R6 INSULIN HEXAMER
I: R6 INSULIN HEXAMER
J: R6 INSULIN HEXAMER
K: R6 INSULIN HEXAMER
L: R6 INSULIN HEXAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,60120
Polymers34,90612
Non-polymers6958
Water362
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30LOWEST TOTAL ENERGY
Representative

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Components

#1: Protein/peptide
R6 INSULIN HEXAMER


Mass: 2383.698 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PANCREAS / References: UniProt: P01308
#2: Protein/peptide
R6 INSULIN HEXAMER


Mass: 3433.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PANCREAS / References: UniProt: P01308
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Zinc
#4: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O / Phenol
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1 / Solution-ID: 1

Experiment-IDType
12D DQF-COSY
2NOESY AND TOCSY
32D 13C-1H HSQC
4HSQC-TOCSY
53D TOCSY-NOESY

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Sample preparation

Sample conditionspH: 8.0 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AM500BrukerAM5005001
Varian UNITY INOVA PLUSVarianUNITY INOVA PLUS7502

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software

Name: X-PLOR

VersionDeveloperClassification
3.1BRUNGERrefinement
structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, ENERGY MINIMIZATION
Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST TOTAL ENERGY / Conformers calculated total number: 30 / Conformers submitted total number: 10

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