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- PDB-4aiy: R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'GREEN' SUBSTATE, AVER... -

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Basic information

Entry
Database: PDB / ID: 4aiy
TitleR6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'GREEN' SUBSTATE, AVERAGE STRUCTURE
Components(PROTEIN (INSULIN)) x 2
KeywordsHORMONE/GROWTH FACTOR / HORMONE / GLUCOSE METABOLISM / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / activation of protein kinase B activity / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import across plasma membrane / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / cognition / vasodilation / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / 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
MethodSOLUTION NMR / SYMMETRY-ADR METHOD: SIMULATED ANNEALING, WATER-SHELL REFINEMENT, AND ENERGY MINIMIZATION
Model type detailsminimized average
AuthorsO'Donoghue, S.I. / Chang, X. / Abseher, R. / Nilges, M. / Led, J.J.
Citation
Journal: J.Biomol.NMR / Year: 2000
Title: Unraveling the symmetry ambiguity in a hexamer: calculation of the R6 human insulin structure.
Authors: O'Donoghue, S.I. / Chang, X. / Abseher, R. / Nilges, M. / Led, J.J.
#1: Journal: Structure, Computation and Dynamics in Protein NMR (in: Biological Magnetic Resonance, V. 17)
Year: 1999
Title: Calculation of Symmetric Oligomer Structures from NMR Data
Authors: O'Donoghue, S.I. / Nilges, M.
#2: Journal: Biochemistry / Year: 1997
Title: Solution Structures of the R6 Human Insulin Hexamer
Authors: Chang, X. / Jorgensen, A.M. / Bardrum, P. / Led, J.J.
History
DepositionDec 29, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (INSULIN)
B: PROTEIN (INSULIN)
C: PROTEIN (INSULIN)
D: PROTEIN (INSULIN)
E: PROTEIN (INSULIN)
F: PROTEIN (INSULIN)
G: PROTEIN (INSULIN)
H: PROTEIN (INSULIN)
I: PROTEIN (INSULIN)
J: PROTEIN (INSULIN)
K: PROTEIN (INSULIN)
L: PROTEIN (INSULIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,47118
Polymers34,90612
Non-polymers5656
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 40LOWEST TOTAL ENERGY
Representativeminimized average structure

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Components

#1: Protein/peptide
PROTEIN (INSULIN)


Mass: 2383.698 Da / Num. of mol.: 6 / Fragment: ALPHA CHAIN / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED FROM THE SECRETION OF HUMAN (HOMO SAPIENS) PANCREATIC CELLS.
References: UniProt: P01308
#2: Protein/peptide
PROTEIN (INSULIN)


Mass: 3433.953 Da / Num. of mol.: 6 / Fragment: BETA CHAIN / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED FROM THE SECRETION OF HUMAN (HOMO SAPIENS) PANCREATIC CELLS.
References: UniProt: P01308
#3: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
121NOESY AND TOCSY
1312D 13C-1H HSQC
141HSQC-TOCSY
1513D TOCSY-NOESY

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Sample preparation

DetailsContents: H2O AND D2O
Sample conditionspH: 8 / Pressure: 1 atm / 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

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: SYMMETRY-ADR METHOD: SIMULATED ANNEALING, WATER-SHELL REFINEMENT, AND ENERGY MINIMIZATION
Software ordinal: 1
Details: REFINEMENT WAS DONE IN A SHELL OF WATER MOLECULES (J.P.LINGE,M.NILGES,1998, J.BIOMOL.NMR, IN PRESS).
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: LOWEST TOTAL ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 1

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