SASDEX5: Albumin-insulin detemir 1:6 complex, binding in Südlow's Site I

Basic information

• Entry: Database: SASBDB / ID: SASDEX5

Sample

Albumin-insulin detemir 1:6 complex, binding in Südlow's Site I

• Insulin detemir (Levemir(R), Novo Nordisk A/S) (protein)
• Human Albumin (Recombumin(R) Alpha, Albumedix Ltd.) (protein)

Function / homology

Function:

exogenous protein binding / cellular response to calcium ion starvation / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / 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 / Aspirin ADME / Insulin processing / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / antioxidant activity / Regulation of gene expression in beta cells / positive regulation of respiratory burst / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / toxic substance binding / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / negative regulation of protein secretion / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / Scavenging of heme from plasma / positive regulation of nitric oxide mediated signal transduction / fatty acid homeostasis / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / Recycling of bile acids and salts / 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 / cellular response to starvation / 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 / platelet alpha granule lumen / Regulation of insulin secretion / positive regulation of long-term synaptic potentiation / endosome lumen / fatty acid binding / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of nitric-oxide synthase activity / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / Post-translational protein phosphorylation / regulation of synaptic plasticity / wound healing / insulin receptor binding / hormone activity / negative regulation of protein catabolic process / Cytoprotection by HMOX1 / cognition / positive regulation of neuron projection development / Golgi lumen / positive regulation of protein localization to nucleus / vasodilation / glucose metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / regulation of protein localization / glucose homeostasis / pyridoxal phosphate binding / cell-cell signaling / Platelet degranulation / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-folding chaperone binding / positive regulation of cell growth / secretory granule lumen / blood microparticle / protease binding

Domain/homology:

Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / 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

Component:

Insulin / Albumin

• Citation: Journal: Acta Crystallogr D Struct Biol / Year: 2019; Title: Solution structures of long-acting insulin analogues and their complexes with albumin.; Authors: Line A Ryberg / Pernille Sønderby / Fabian Barrientos / Jens T Bukrinski / Günther H J Peters / Pernille Harris / ; Abstract: The lipidation of peptide drugs is one strategy to obtain extended half-lives, enabling once-daily or even less frequent injections for patients. The half-life extension results from a combination of self-association and association with human serum albumin (albumin). The self-association and association with albumin of two insulin analogues, insulin detemir and insulin degludec, were investigated by small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) in phenolic buffers. Detemir shows concentration-dependent self-association, with an equilibrium between hexamer, dihexamer, trihexamer and larger species, while degludec appears as a dihexamer independent of concentration. The solution structure of the detemir trihexamer has a bent shape. The stoichiometry of the association with albumin was studied using DLS. For albumin-detemir the molar stoichiometry was determined to be 1:6 (albumin:detemir ratio) and for albumin-degludec it was between 1:6 and 1:12 (albumin:degludec ratio). Batch SAXS measurements of a 1:6 albumin:detemir concentration series revealed a concentration dependence of complex formation. The data allowed the modelling of a complex between albumin and a detemir hexamer and a complex consisting of two albumins binding to opposite ends of a detemir dihexamer. Measurements of size-exclusion chromatography coupled to SAXS revealed a complex between a degludec dihexamer and albumin. Based on the results, equilibria for the albumin-detemir and albumin-degludec mixtures are proposed.

Contact author

• Line Abildgaard Ryberg (Technical University of Denmark, Lyngby, Denmark)

Models

• Model #2459: ; Type: atomic / Chi-square value: 0.93 / P-value: 0.000181; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2460: ; Type: dummy / Radius of dummy atoms: 2.70 A / Chi-square value: 0.855 / P-value: 0.000022; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Albumin-insulin detemir 1:6 complex, binding in Südlow's Site I; Specimen concentration: 8.5 mg/ml / Entity id: 1319 / 1320
• Buffer: Name: 6.9 mM Na2HPO4, 11.9 mM m-cresol, 13.7 mM phenol, 157.3 mM glycerol, 38.5 mM NaCl; pH: 7.4

Entity #1319

Type: protein / Description: Insulin detemir (Levemir(R), Novo Nordisk A/S) / Formula weight: 5.9 / Num. of mol.: 6 / References: UniProt: P01308
Sequence:

GIVEQCCTSI CSLYQLENYC NFVNQHLCGS HLVEALYLVC GERGFFYTPK

Entity #1320

Type: protein
Description: Human Albumin (Recombumin(R) Alpha, Albumedix Ltd.)
Formula weight: 66.472 / Num. of mol.: 1 / References: UniProt: P02768
Sequence:

DAHKSEVAHR FKDLGEENFK ALVLIAFAQY LQQCPFEDHV KLVNEVTEFA KTCVADESAE NCDKSLHTLF GDKLCTVATL RETYGEMADC CAKQEPERNE CFLQHKDDNP NLPRLVRPEV DVMCTAFHDN EETFLKKYLY EIARRHPYFY APELLFFAKR YKAAFTECCQ AADKAACLLP KLDELRDEGK ASSAKQRLKC ASLQKFGERA FKAWAVARLS QRFPKAEFAE VSKLVTDLTK VHTECCHGDL LECADDRADL AKYICENQDS ISSKLKECCE KPLLEKSHCI AEVENDEMPA DLPSLAADFV ESKDVCKNYA EAKDVFLGMF LYEYARRHPD YSVVLLLRLA KTYETTLEKC CAAADPHECY AKVFDEFKPL VEEPQNLIKQ NCELFEQLGE YKFQNALLVR YTKKVPQVST PTLVEVSRNL GKVGSKCCKH PEAKRMPCAE DYLSVVLNQL CVLHEKTPVS DRVTKCCTES LVNRRPCFSA LEVDETYVPK EFNAETFTFH ADICTLSEKE RQIKKQTALV ELVKHKPKAT KEQLKAVMDD FAAFVEKCCK ADDKETCFAE EGKKLVAASQ AALGL

Experimental information

• Beam: Instrument name: MAX IV I911-4 / City: Lund / 国: Sweden / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.091 Å / Dist. spec. to detc.: 1.962 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Albumin-insulin detemir 1:6 complex, binding in Südlow's Site I
Measurement date: Sep 25, 2015 / Cell temperature: 20 °C / Exposure time: 30 sec. / Number of frames: 4 / Unit: 1/nm /

	Min	Max
Q	0.0845	5.4054

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 394 /

	Min	Max
Q	0.122541	2.25631
P(R) point	1	394
R	0	13.03

Result

D max: 13.03 / Type of curve: single_conc /

	Experimental	Porod
MW	102.1 kDa	108.2 kDa
Volume	-	162.34 nm3

	P(R)	Guinier
Forward scattering, I0	0.075	0.074
Radius of gyration, Rg	3.64 nm	3.54 nm