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- PDB-1t1q: NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, P... -

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Basic information

Entry
Database: PDB / ID: 1t1q
TitleNMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES
Components
  • Insulin
  • insulin
KeywordsHORMONE/GROWTH FACTOR / Aba-B12-DKP-insulin / protein unfolding / insulin receptor / receptor binding / 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 / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / 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 / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / 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 cytokine production / positive regulation of glycolytic process / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / Regulation of insulin secretion / positive regulation of cell differentiation / 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 / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / 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 / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsHuang, K. / Xu, B. / Hu, S.Q. / Chu, Y.C. / Hua, Q.X. / Whittaker, J. / Nakagawa, S.H. / De Meyts, P. / Katsoyannis, P.G. / Weiss, M.A.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: How Insulin Binds: the B-Chain alpha-Helix Contacts the L1 beta-Helix of the Insulin Receptor.
Authors: Huang, K. / Xu, B. / Hu, S.Q. / Chu, Y.C. / Hua, Q.X. / Qu, Y. / Li, B. / Wang, S. / Wang, R.Y. / Nakagawa, S.H. / Theede, A.M. / Whittaker, J. / De Meyts, P. / Katsoyannis, P.G. / Weiss, M.A.
#1: Journal: Biochemistry / Year: 2000
Title: MUTATIONAL ANALYSIS OF INVARIANT VALINE B12 IN INSULIN: IMPLICATION FOR RECEPTOR BINDING
Authors: Nakagawa, S.H. / Tager, H.S. / Steiner, D.F.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: ALANINE SCANNING MUTAGENESIS OF INSULIN
Authors: Kristen, C. / Kjeldsen, T. / Wiberg, F.C. / Schaffer, L. / Hach, M. / Havelund, S. / Bass, J. / Steiner, D.F. / Andersen, A.S.
#3: Journal: BIOCHEM.MOL.BIOL.INT. / Year: 1996
Title: STUDIES ON RECEPTOR BINDING SITE OF INSULIN: THE HYDROPHOBIC B12VALCAN BE SUBSTITUTED BY HYDROPHILIC THR
Authors: Wang, Q.Q. / Feng, Y.M. / Zhang, Y.S.
#4: Journal: Biochemistry / Year: 1993
Title: STERIC REQUIRMENTS AT POSITION B12 FOR HIGH BIOLOGICAL ACTIVITY IN INSULIN
Authors: Hu, S.Q. / Burke, G.T. / Schwartz, G.P. / Ferderigos, N. / Ross, J.B. / Katsoyannis, P.G.
#5: Journal: INT.J.PEPT.PROTEIN RES. / Year: 1981
Title: [12-ASPARAGINE-B] HUMAN INSULIN. AN ANALOGUE WITH MODIFICATION IN THEHYDROPHOBIC CORE OF INSULIN
Authors: Schwartz, G.P. / Burke, P.G. / Katsoyannis, P.G.
History
DepositionApr 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,7812
Polymers5,7812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 / Fragment: INSULIN A CHAIN
Mutation: HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO
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: 3396.868 Da / Num. of mol.: 1 / Fragment: INSULIN B CHAIN / 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1,2,311,2,32D NOESY
1,2,321,2,32D TOCSY
1,2,331,2,3DQF-COSY
NMR detailsText: This structure was determined by using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM ABA-B12-DKP-insulin, 90% H2O, 10% D2O90% H2O/10% D2O
21.2 mM ABA-B12-DKP-insulin,100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17ambient 298 K
27.6ambient 305 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
DGIIINSIGHTII 2000Molecular Simulations INC.structure solution
X-PLOR3.85Brungerrefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: the structures are based on a total of 590 restraints: 527 are NOE-derived distance constraints, 39 are dihedral angle restraints, 24 are hydrogen bond restraints.
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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