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- PDB-2kju: NMR structure of human insulin mutant glu-b21-d-glu, his-b10 asp ... -

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Basic information

Entry
Database: PDB / ID: 2kju
TitleNMR structure of human insulin mutant glu-b21-d-glu, his-b10 asp pro-b28-lys, lys-b29-pro, 20 structures
Components(Insulin) x 2
KeywordsIMMUNE SYSTEM / HORMONE / HUMAN INSULIN / MUTANT / FIBRILLATION / STABILITY / Carbohydrate metabolism / Cleavage on pair of basic residues / Disulfide bond / Glucose metabolism / Secreted / Diabetes mellitus / Disease mutation / Pharmaceutical
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
Model detailsclosest to the average, model 1
AuthorsHua, Q.X. / Huang, K. / Hu, S.Q. / Katsoyanni, P. / Weiss, M.A.
CitationJournal: To be Published
Title: Acceleration of Protein Fibrillation by Chiral Destabilization of Beta-Turn
Authors: Hua, Q.X. / Huang, K. / Hu, S.Q. / Katsoyanni, P. / Weiss, M.A.
History
DepositionJun 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _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)5,7952
Polymers5,7952
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures 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, residues 90-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin /


Mass: 3410.894 Da / Num. of mol.: 1 / Fragment: Insulin B chain, residues 25-54 / Mutation: HIS10ASP, GLU21DGL, PRO28LYS, LYS29PRO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
Compound detailsINSULIN B-CHAIN MADE VIA SEMI-SYNTHESIS: EXPRESSED INSULIN B-CHAIN WAS DIGEST THEN MERGED WITH ...INSULIN B-CHAIN MADE VIA SEMI-SYNTHESIS: EXPRESSED INSULIN B-CHAIN WAS DIGEST THEN MERGED WITH ORGANIC SYNTHESIZED PART OF B-CHAIN (CONTAINED B21-D-GLU).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121NOESY
131COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES.

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Sample preparation

DetailsContents: 0.5 mM INSULIN A CHAIN, 0.5 mM INSULIN B CHAIN, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMINSULIN A CHAIN-11
0.5 mMINSULIN B CHAIN-21
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 7.0 1 bar298 K
20.1 2.0 1 bar298 K
30.1 7.6 1 bar305 K

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NMR measurement

NMR spectrometerType: BRUKER DRX / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.85BRUNGERrefinement
XwinNMR3.5Bruker Biospinstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: RMSD VALUES FOR ALL 20 STRUCTURES VERSUS GEOMETRIC AVERAGE: (BACKBONE, A2-A20, B4-B24) 0.42 ANGSTROM
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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