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- PDB-2kqq: NMR structure of human insulin mutant gly-b8-d-ala, his-b10-asp, ... -

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Basic information

Entry
Database: PDB / ID: 2kqq
TitleNMR structure of human insulin mutant gly-b8-d-ala, his-b10-asp, pro-b28-lys, lys-b29-pro, 20 structures
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / HUMAN INSULIN / MUTANT / D-Alanine substitution / protein stability / dynamics
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 / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / 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 / positive regulation of protein autophosphorylation / transport vesicle / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / activation of protein kinase B activity / 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 / Regulation of insulin secretion / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED
Model detailsclosest to the average, model 1
AuthorsHua, Q.X. / Wan, Z.L. / Zhao, M. / Jia, W. / Huang, K. / Weiss, M.A.
CitationJournal: To be Published
Title: Structure and Dynamics of an Turn-Stabilize But Ina Insulin Analog.
Authors: Hua, Q.X. / Wan, Z.L. / Zhao, M. / Jia, W. / Huang, K. / Weis, M.A.
History
DepositionNov 13, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_cs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,8092
Polymers5,8092
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)20 / 40STRUCTURES WITH THE LOWEST ENERG
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Insulin B chain / Insulin B chain / Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 1
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 A chain / Insulin B chain / Insulin A chain


Mass: 3424.920 Da / Num. of mol.: 1 / Mutation: G8Dal, H10D, P28K, K29P
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

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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: 0.5-0.8 mM entity_1-1, 0.5-0.8 mM entity_2-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentConc. range (mg/ml)Solution-ID
mMentity_1-10.5-0.81
mMentity_2-20.5-0.81
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: AMBIENT / Temperature: 298 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
VNMR3.5Varianstructure solution
VNMR3.5Varianrefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LOWEST ENERG
Conformers calculated total number: 40 / Conformers submitted total number: 20

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