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- PDB-2juv: AbaA3-DKP-insulin -

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Basic information

Entry
Database: PDB / ID: 2juv
TitleAbaA3-DKP-insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin / Aba / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Glucose metabolism / Pharmaceutical / Secreted
Function / homology
Function and homology information


Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic 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 ...Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic 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 / regulation of cellular amino acid metabolic process / negative regulation of acute inflammatory response / negative regulation of reactive oxygen species biosynthetic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / Regulation of insulin secretion / 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 protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of insulin receptor signaling pathway / endosome lumen / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / positive regulation of cell differentiation / regulation of transmembrane transporter activity / Insulin receptor signalling cascade / 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 / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / vasodilation / insulin receptor signaling pathway / Golgi lumen / glucose metabolic process / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / 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 / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Golgi membrane / Amyloid fiber formation / 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-like / Insulin / insulin-like growth factor / relaxin family. / Insulin family signature. / Insulin, conserved site / Insulin-like superfamily
Similarity search - Domain/homology
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsHuang, K. / Chan, S. / Hua, Q. / Chu, Y. / Wang, R. / Klaproth, B. / Jia, W. / Whittaker, J. / De Meyts, P. / Nakagawa, S.H. ...Huang, K. / Chan, S. / Hua, Q. / Chu, Y. / Wang, R. / Klaproth, B. / Jia, W. / Whittaker, J. / De Meyts, P. / Nakagawa, S.H. / Steiner, D.F. / Katsoyannis, P.G. / Weiss, M.A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The A-chain of Insulin Contacts the Insert Domain of the Insulin Receptor: PHOTO-CROSS-LINKING AND MUTAGENESIS OF A DIABETES-RELATED CREVICE.
Authors: Huang, K. / Chan, S.J. / Hua, Q.X. / Chu, Y.C. / Wang, R.Y. / Klaproth, B. / Jia, W. / Whittaker, J. / De Meyts, P. / Nakagawa, S.H. / Steiner, D.F. / Katsoyannis, P.G. / Weiss, M.A.
History
DepositionSep 5, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)5,7812
Polymers5,7812
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Insulin A chain


Mass: 2369.672 Da / Num. of mol.: 1 / Mutation: V3T / Source method: obtained synthetically / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3410.894 Da / Num. of mol.: 1 / Mutation: H10D,P28K,K29P / Source method: obtained synthetically / 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 COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
2422D 1H-1H COSY
2522D 1H-1H TOCSY
2622D 1H-1H NOESY
3732D 1H-1H COSY
3832D 1H-1H TOCSY
3932D 1H-1H NOESY
21042D DQF-COSY
21142D 1H-1H TOCSY
21242D 1H-1H NOESY
21352D DQF-COSY
21452D 1H-1H TOCSY
21552D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM AbaA3-DKP-insulin, 90% H2O/10% D2O90% H2O/10% D2O
21 mM AbaA3-DKP-insulin, 100% D2O100% D2O
31 mM AbaA3-DKP-insulin, 100% D2O100% D2O
41 mM AbaA3-DKP-insulin, 20% D-acetic acid/80% H2O20% D-acetic acid/80% H2O
51 mM AbaA3-DKP-insulin, 20%D-acetic acid/80% D2O20%D-acetic acid/80% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMAbaA3-DKP-insulin1
1 mMAbaA3-DKP-insulin2
1 mMAbaA3-DKP-insulin3
1 mMAbaA3-DKP-insulin4
1 mMAbaA3-DKP-insulin5
Sample conditions
Conditions-IDpHPressure (Pa)Temperature (K)
17.0 ambient 308 K
28.0 ambient 315 K
31.9 ambient 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNSAccelrysrefinement
X-PLOR3.1Brunger, A.T. et al.refinement
RefinementMethod: DGSA-distance geometry 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: 50 / Conformers submitted total number: 15

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