8RRP | pdb_00008rrp

Insulin Icodec - A14E B16H B25H B29Ne-C20 diacid-LgGlu-2xAdo desB30 human insulin

• PDB DOI: https://doi.org/10.2210/pdb8RRP/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2024-01-23 Released: 2024-07-10 
• Deposition Author(s): Schluckebier, G., Johansson, E.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Enhanced disulphide bond stability contributes to the once-weekly profile of insulin icodec.

Hubalek, F., Cramer, C.N., Helleberg, H., Johansson, E., Nishimura, E., Schluckebier, G., Steensgaard, D.B., Sturis, J., Kjeldsen, T.B.

(2024) Nat Commun 15: 6124-6124

• PubMed: 39033137 
• DOI: https://doi.org/10.1038/s41467-024-50477-9
• Primary Citation Related Structures: 
  8RRP


• PubMed Abstract: 
  

  Insulin icodec is a once-weekly insulin analogue that has a long half-life of approximately 7 days, making it suitable for once weekly dosing. The Insulin icodec molecule was developed based on the hypothesis that lowering insulin receptor affinity and introducing a strong albumin-binding moiety would result in a long insulin half-life, provided that non-receptor-mediated clearance is diminished. Here, we report an insulin clearance mechanism, resulting in the splitting of insulin molecules into its A-chain and B-chain by a thiol-disulphide exchange reaction. Even though the substitutions in insulin icodec significantly stabilise insulin against such degradation, some free B-chain is observed in plasma samples from minipigs and people with type 2 diabetes. In summary, we identify thiol-disulphide exchange reactions to be an important insulin clearance mechanism and find that stabilising insulin icodec towards this reaction significantly contributes to its long pharmacokinetic/pharmacodynamic profile.

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Organizational Affiliation: 
• Novo Nordisk A/S, Maaloev, Denmark. [e-mail].
Novo Nordisk A/S, Maaloev, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 17.06 kDa 
• Atom Count: 1,217 
• Modeled Residue Count: 147 
• Deposited Residue Count: 150 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin	A, C, E	21	Homo sapiens	Mutation(s): 1  Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin B chain	B, D, F	29	Homo sapiens	Mutation(s): 2  Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	G [auth B], H [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.793	α = 90
b = 54.793	β = 90
c = 138.355	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Schluckebier, G., Johansson, E.

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Funding Organization	Location	Grant Number
Other private	Denmark	--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2024-07-31
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary