SASDEY5: Albumin-insulin detemir 2:12 complex, P1 symmetry (Human Albumin ...

Basic information

• Entry: Database: SASBDB / ID: SASDEY5

Sample

Albumin-insulin detemir 2:12 complex, P1 symmetry

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

Function / homology

Function:

Ciprofloxacin ADME / cellular response to calcium ion starvation / exogenous protein binding / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / negative regulation of NAD(P)H oxidase activity / Prednisone ADME / Heme degradation / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / regulation of protein secretion / Insulin processing / Aspirin ADME / positive regulation of peptide hormone secretion / antioxidant activity / Regulation of gene expression in beta cells / positive regulation of respiratory burst / negative regulation of acute inflammatory response / alpha-beta T cell activation / regulation of amino acid metabolic process / positive regulation of dendritic spine maintenance / negative regulation of respiratory burst involved in inflammatory response / Synthesis, secretion, and deacylation of Ghrelin / toxic substance binding / negative regulation of protein secretion / negative regulation of gluconeogenesis / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Scavenging of heme from plasma / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / positive regulation of insulin receptor signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Recycling of bile acids and salts / positive regulation of protein autophosphorylation / nitric oxide-cGMP-mediated signaling / COPI-mediated anterograde transport / activation of protein kinase B activity / transport vesicle / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / platelet alpha granule lumen / positive regulation of glycolytic process / cellular response to starvation / fatty acid binding / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / negative regulation of proteolysis / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / Post-translational protein phosphorylation / insulin receptor binding / regulation of transmembrane transporter activity / wound healing / Cytoprotection by HMOX1 / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / Golgi lumen / positive regulation of protein localization to nucleus / cognition / glucose metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / vasodilation / pyridoxal phosphate binding / insulin receptor signaling pathway / glucose homeostasis / Platelet degranulation / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / regulation of protein localization / protein-folding chaperone binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / blood microparticle

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-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / 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 #2462: ; Type: atomic / Chi-square value: 1.008 / P-value: 0.000003; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2463: ; Type: dummy / Radius of dummy atoms: 2.70 A / Chi-square value: 0.828 / P-value: 0.000106; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Albumin-insulin detemir 2:12 complex, P1 symmetry / Specimen concentration: 15.6 mg/ml / Entity id: 1320 / 1321
• Buffer: Name: 8.8 mM Na2HPO4, 10.6 mM m-cresol, 12.2 mM phenol, 140.9 mM glycerol, 56.9 mM NaCl; pH: 7.4

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

Entity #1321

Type: protein / Description: Insulin detemir (Levemir(R), Novo Nordisk A/S) / Formula weight: 5.9 / Num. of mol.: 12 / References: UniProt: P01308
Sequence:

GIVEQCCTSI CSLYQLENYC NFVNQHLCGS HLVEALYLVC GERGFFYTPK

Experimental information

• Beam: Instrument name: MAX IV I911-4 / City: Lund / 国: Sweden / Type of source: X-ray synchrotron / 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 2:12 complex, P1 symmetry / 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: 243 /

	Min	Max
Q	0.160547	1.47447
P(R) point	1	243
R	0	19.5

Result

D max: 19.5 / Type of curve: single_conc /

	Experimental	Porod
MW	208.3 kDa	206.3 kDa
Volume	-	309.45 nm3

	P(R)	Guinier
Forward scattering, I0	0.1522	0.15
Radius of gyration, Rg	5.694 nm	5.41 nm