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- PDB-5wbt: Solution Structure and Dynamics of an Ultra-Stable Single-Chain I... -

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Basic information

Entry
Database: PDB / ID: 5wbt
TitleSolution Structure and Dynamics of an Ultra-Stable Single-Chain Insulin Analog STUDIES OF AN ENGINEERED MONOMER AND IMPLICATIONS FOR RECEPTOR BINDING
ComponentsInsulin
KeywordsHORMONE / heat-stable
Function / homology
Function and homology information


Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / negative regulation of reactive oxygen species biosynthetic process / positive regulation of cellular protein metabolic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / Regulation of insulin secretion / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / regulation of cellular amino acid metabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / fatty acid homeostasis / endosome lumen / transport vesicle / positive regulation of insulin receptor signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / negative regulation of acute inflammatory response / regulation of transmembrane transporter activity / positive regulation of cell differentiation / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / regulation of synaptic plasticity / positive regulation of brown fat cell differentiation / cognition / regulation of protein localization / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / vasodilation / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / insulin receptor signaling pathway / glucose metabolic process / Golgi lumen / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of MAPK cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell migration / positive regulation of protein kinase B signaling / Amyloid fiber formation / Golgi membrane / G protein-coupled receptor signaling pathway / amyloid fibril formation / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin-like, subunit E / Insulin-like / Insulin / Insulin family / Insulin / insulin-like growth factor / relaxin family. / Insulin-like / Insulin/IGF/Relaxin family / Insulin-like superfamily / Insulin, conserved site / Insulin family signature. ...Insulin-like, subunit E / Insulin-like / Insulin / Insulin family / Insulin / insulin-like growth factor / relaxin family. / Insulin-like / Insulin/IGF/Relaxin family / Insulin-like superfamily / Insulin, conserved site / Insulin family signature. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGlidden, M.D. / Yang, Y. / Wickramasinghe, N.P. / Weiss, M.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK040949 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK069764 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1F30DK104618-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM007250-38 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Solution structure of an ultra-stable single-chain insulin analog connects protein dynamics to a novel mechanism of receptor binding.
Authors: Glidden, M.D. / Yang, Y. / Smith, N.A. / Phillips, N.B. / Carr, K. / Wickramasinghe, N.P. / Ismail-Beigi, F. / Lawrence, M.C. / Smith, B.J. / Weiss, M.A.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin


Theoretical massNumber of molelcules
Total (without water)6,5151
Polymers6,5151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4080 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 98structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein Insulin /


Mass: 6515.308 Da / Num. of mol.: 1 / Fragment: residues 25-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Pichia (fungus) / References: UniProt: P01308

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic14D Time-shared NOESY
121isotropic13D HNCA
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HN(CA)CB
161isotropic13D HN(CO)CA
191isotropic13D HCC-TOCSY
181isotropic13D H(CCO)NH
171isotropic13D 1H-15N TOCSY
1161isotropic13D (H)CC(CO)NH
1151isotropic12D 1H-15N HSQC
1141isotropic12D 1H-13C HSQC
1131isotropic12D 1H-13C HSQC aromatic

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] Single chain insulin SCI-b, 90% H2O/10% D2O
Label: 15N_13C_Sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Single chain insulin SCI-b / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: pH 7.4 and 25C / Ionic strength: 0 M / Label: conditions_1 / pH: 7.4 / 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
X-PLORBRUNGERrefinement
Sparkystructure solution
TopSpinstructure solution
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: TIME AVERAGED NOE RESTRAINED MOLECULAR DYNAMICS; TIME AVERAGING FOR RESIDUES 1-5 AND 28-36 ONLY
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 98 / Conformers submitted total number: 19

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