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- PDB-6u46: Solution Structure of a Heat-Resistant Long-Acting Insulin Analog -

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Basic information

Entry
Database: PDB / ID: 6u46
TitleSolution Structure of a Heat-Resistant Long-Acting Insulin Analog
ComponentsInsulin
KeywordsHORMONE / protein design / Heat-resistant insulin
Function / homology
Function and homology information


: / negative regulation of glycogen catabolic process / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / negative regulation of acute inflammatory response ...: / negative regulation of glycogen catabolic process / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / negative regulation of acute inflammatory response / positive regulation of respiratory burst / Regulation of gene expression in beta cells / alpha-beta T cell activation / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of gluconeogenesis / negative regulation of protein secretion / fatty acid homeostasis / positive regulation of brown fat cell differentiation / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / positive regulation of insulin receptor signaling pathway / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / nitric oxide-cGMP-mediated signaling / regulation of protein localization to plasma membrane / transport vesicle / Insulin receptor recycling / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of D-glucose import across plasma membrane / positive regulation of mitotic nuclear division / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / Insulin receptor signalling cascade / endosome lumen / positive regulation of protein secretion / acute-phase response / positive regulation of cytokine production / wound healing / insulin receptor binding / positive regulation of long-term synaptic potentiation / positive regulation of neuron projection development / glucose metabolic process / positive regulation of cell differentiation / negative regulation of protein catabolic process / Regulation of insulin secretion / hormone activity / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / vasodilation / Golgi lumen / cognition / insulin receptor signaling pathway / glucose homeostasis / regulation of protein localization / cell-cell signaling / positive regulation of cell growth / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / secretory granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / receptor ligand activity / Amyloid fiber formation / negative regulation of gene expression / Golgi membrane / positive regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / : / 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 / simulated annealing
AuthorsYang, Y. / Weiss, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: Solution Structure of a Heat-Resistant Long-Acting Insulin Analog
Authors: Weiss, M.A. / Yang, Y.
History
DepositionAug 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin


Theoretical massNumber of molelcules
Total (without water)6,7881
Polymers6,7881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 98structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Insulin


Mass: 6787.704 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P01308*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-15N TOCSY
131isotropic12D 1H-15N HSQC
142anisotropic12D 1H-1H TOCSY
152anisotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 15N] insulin, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21 mM unlabled Single-chain insulin, 90% H2O/10% D2Ounlabled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMinsulin[U-99% 15N]1
1 mMSingle-chain insulinunlabled2
Sample conditionsIonic strength: 0 mM / Label: condition_1 / pH: 3.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
PIPPGarrettdata analysis
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 98 / Conformers submitted total number: 20

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