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- PDB-1kmf: NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALLO-ILE, HIS-B10-AS... -

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Basic information

Entry
Database: PDB / ID: 1kmf
TitleNMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALLO-ILE, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES
Components(Insulin) x 2
KeywordsHORMONE/GROWTH FACTOR / Hormone / Human insulin / Mutant / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / 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 / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / 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 / Insulin processing / regulation of protein secretion / 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 / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / negative regulation of proteolysis / positive regulation of D-glucose import / positive regulation of protein secretion / Regulation of insulin secretion / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / negative regulation of protein catabolic process / regulation of synaptic plasticity / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / 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 / Distance geometry, simulated annealing
AuthorsXu, B. / Hua, Q.X. / Nakagawa, S.H. / Jia, W. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Chiral mutagenesis of insulin's hidden receptor-binding surface: structure of an allo-isoleucine(A2) analogue.
Authors: Xu, B. / Hua, Q.X. / Nakagawa, S.H. / Jia, W. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A.
#1: Journal: Biochemistry / Year: 1984
Title: Critical Role of the A2 Amino Acid Residue in the Biological Activity of Insulin: [2-Glycine-A]- and [2-Alanine-A]insulins
Authors: Kitagawa, K. / Ogawa, H. / Burke, G.T. / Chanley, J.D. / Katsoyannis, P.G.
#2: Journal: Biochemistry / Year: 1992
Title: Importance of Aliphatic Side-Chain Structure at Positions 2 and 3 of the Insulin A Chain in Insulin-Receptor Interactions
Authors: Nakagawa, S.H. / Tager, H.S.
#3: Journal: J.Mol.Biol. / Year: 1996
Title: Mapping the Functional Surface of Insulin by Design: Structure and Function of a Novel A-Chain Analogue
Authors: Hua, Q.X. / Hu, S.Q. / Frank, B.H. / Jia, W. / Chu, Y.C. / Wang, S.H. / Burke, G.T. / Katsoyannis, P.G. / Weiss, M.A.
#4: Journal: Protein Sci. / Year: 2002
Title: A Cavity-Forming Mutation in Insulin Induces Segmental Unfolding of a Surrounding alpha-Helix
Authors: Xu, B. / Hua, Q.X. / Nakagawa, S.H. / Jia, W. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A.
History
DepositionDec 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,7952
Polymers5,7952
Non-polymers00
Water00
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


Mass: 2383.698 Da / Num. of mol.: 1 / Mutation: I2(IIL) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P01308
#2: Protein/peptide Insulin


Mass: 3410.894 Da / Num. of mol.: 1 / Mutation: H10D, P28K, K29P / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P01308
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
2312D NOESY
241DQF-COSY
2522D NOESY
262DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM Allo-Ile-A2-DKP-insulin; 90% H2O, 10% D2O90% H2O/10% D2O
21.2 mM Allo-Ile-A2-DKP-insulin; 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17ambient 298 K
27.6ambient 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DGIIInsightII 2000Molecular Simulations Inc.refinement
X-PLOR3.85Brungerrefinement
RefinementMethod: Distance geometry, simulated annealing / Software ordinal: 1
Details: The structure is based on a total of 599 restraints, 542 are NOE-derived distance constraints, 38 dihedral angle restraints, 19 distance restraints from hydrogen bonds.
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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