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- PDB-8rrp: Insulin Icodec - A14E B16H B25H B29Ne-C20 diacid-LgGlu-2xAdo desB... -

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Basic information

Entry
Database: PDB / ID: 8rrp
TitleInsulin Icodec - A14E B16H B25H B29Ne-C20 diacid-LgGlu-2xAdo desB30 human insulin
Components
  • Insulin
  • Insulin B chain
KeywordsHORMONE / Insulin
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 / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / 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 / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / negative regulation of proteolysis / positive regulation of D-glucose import / positive regulation of protein secretion / Regulation of insulin secretion / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / negative regulation of protein catabolic process / regulation of synaptic plasticity / 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
ACETATE ION / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchluckebier, G. / Johansson, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Other private Denmark
CitationJournal: Nat Commun / Year: 2024
Title: Enhanced disulphide bond stability contributes to the once-weekly profile of insulin icodec.
Authors: Hubalek, F. / Cramer, C.N. / Helleberg, H. / Johansson, E. / Nishimura, E. / Schluckebier, G. / Steensgaard, D.B. / Sturis, J. / Kjeldsen, T.B.
History
DepositionJan 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin
B: Insulin B chain
C: Insulin
D: Insulin B chain
E: Insulin
F: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0638
Polymers16,9456
Non-polymers1182
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-61 kcal/mol
Surface area7330 Å2
Unit cell
Length a, b, c (Å)54.793, 54.793, 138.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein/peptide Insulin


Mass: 2349.638 Da / Num. of mol.: 3 / Mutation: Y14E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3298.795 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.02 calcium chloride 30 % 2-methyl-2,4-pentanediol 0.1M acetate pH4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 28, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→29.67 Å / Num. obs: 14970 / % possible obs: 99.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 35.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.02 / Rrim(I) all: 0.29 / Net I/σ(I): 28.48
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.43 / Num. unique obs: 1461 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.1751 / Rrim(I) all: 0.2476 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.67 Å / SU ML: 0.1711 / Cross valid method: FREE R-VALUE / Phase error: 23.1236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 2705 10.01 %
Rwork0.1786 24329 -
obs0.1825 14918 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.71 Å2
Refinement stepCycle: LAST / Resolution: 2→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 8 50 1209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01141187
X-RAY DIFFRACTIONf_angle_d1.04851606
X-RAY DIFFRACTIONf_chiral_restr0.0539180
X-RAY DIFFRACTIONf_plane_restr0.0076213
X-RAY DIFFRACTIONf_dihedral_angle_d5.9789159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.27761480.2381306X-RAY DIFFRACTION98.18
2.04-2.080.22861400.20831233X-RAY DIFFRACTION98.64
2.08-2.120.22771400.20371270X-RAY DIFFRACTION99.09
2.12-2.160.29141450.20251276X-RAY DIFFRACTION99.23
2.16-2.210.23461430.20431281X-RAY DIFFRACTION99.1
2.21-2.270.25811410.19851275X-RAY DIFFRACTION98.81
2.27-2.330.23281340.18691274X-RAY DIFFRACTION99.51
2.33-2.40.22871460.17361294X-RAY DIFFRACTION99.93
2.4-2.480.17841380.15951280X-RAY DIFFRACTION99.58
2.48-2.570.20511420.15741276X-RAY DIFFRACTION99.23
2.57-2.670.26811410.16831293X-RAY DIFFRACTION99.79
2.67-2.790.24081480.18021274X-RAY DIFFRACTION99.72
2.79-2.940.18661420.18621276X-RAY DIFFRACTION99.79
2.94-3.120.24521420.1671282X-RAY DIFFRACTION99.72
3.12-3.360.20991420.16261292X-RAY DIFFRACTION99.51
3.36-3.70.19771520.17041296X-RAY DIFFRACTION100
3.7-4.230.18761430.1591277X-RAY DIFFRACTION100
4.24-5.320.19971360.17231280X-RAY DIFFRACTION99.79
5.33-29.670.24281420.2111294X-RAY DIFFRACTION99.93

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