SASDEZ5: Albumin-insulin detemir 2:12 complex, P2 symmetry (Human Albumin ...

Basic information

• Entry: Database: SASBDB / ID: SASDEZ5

Sample

Albumin-insulin detemir 2:12 complex, P2 symmetry

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

Function / homology

Function:

exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / 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 / 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 / Aspirin ADME / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / antioxidant activity / 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 / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / toxic substance binding / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Scavenging of heme from plasma / 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 / Recycling of bile acids and salts / positive regulation of protein autophosphorylation / Insulin receptor recycling / transport vesicle / insulin-like growth factor receptor binding / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / activation of protein kinase B activity / cellular response to starvation / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / platelet alpha granule lumen / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / Regulation of insulin secretion / fatty acid binding / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / Post-translational protein phosphorylation / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / Cytoprotection by HMOX1 / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / glucose metabolic process / pyridoxal phosphate binding / Platelet degranulation / cell-cell signaling / insulin receptor signaling pathway / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / 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 #2465: ; Type: atomic / Chi-square value: 1.115 / P-value: 0.000021; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2467: ; Type: dummy / Radius of dummy atoms: 4.20 A / Chi-square value: 0.887 / P-value: 0.000107; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Albumin-insulin detemir 2:12 complex, P2 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, P2 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