Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12238.56 
• Atom Count: 837 
• Residue Count: 100 
• Unique protein chains: 2

4AKJ

Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin

• DOI: 10.2210/pdb4AKJ/pdb

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


• Deposited: 2012-02-23 Released: 2013-01-09 
• Deposition Author(s): Steensgaard, D.B., Schluckebier, G., Strauss, H.M., Norrman, M., Thomsen, J.K., Friderichsen, A.V., Havelund, S., Jonassen, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 

Literature

Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures by the Engineered Acylated Insulin Degludec.

Steensgaard, D.B., Schluckebier, G., Strauss, H.M., Norrman, M., Thomsen, J.K., Friderichsen, A.V., Havelund, S., Jonassen, I.

(2013) Biochemistry 52: 295

• PubMed: 23256685 
• DOI: 10.1021/bi3008609
• Primary Citation of Related Structures:  
  4AJZ, 4AK0, 4AJX


• PubMed Abstract: 
  

Insulin degludec, an engineered acylated insulin, was recently reported to form a soluble depot after subcutaneous injection with a subsequent slow release of insulin and an ultralong glucose-lowering effect in excess of 40 h in humans. We describe the structure, ligand binding properties, and self-assemblies of insulin degludec using orthogonal structural methods. The protein fold adopted by insulin degludec is very similar to that of human insulin. Hexamers in the R(6) state similar to those of human insulin are observed for insulin degludec in the presence of zinc and resorcinol. However, under conditions comparable to the pharmaceutical formulation comprising zinc and phenol, insulin degludec forms finite dihexamers that are composed of hexamers in the T(3)R(3) state that interact to form an R(3)T(3)-T(3)R(3) structure. When the phenolic ligand is depleted and the solvent condition thereby mimics that of the injection site, the quaternary structure changes from dihexamers to a supramolecular structure composed of linear arrays of hundreds of hexamers in the T(6) state and an average molar mass, M(0), of 59.7 × 10(3) kg/mol. This novel concept of self-assemblies of insulin controlled by zinc and phenol provides the basis for the slow action profile of insulin degludec. To the best of our knowledge, this report for the first time describes a tight linkage between quaternary insulin structures of hexamers, dihexamers, and multihexamers and their allosteric state and its origin in the inherent propensity of the insulin hexamer for allosteric half-site reactivity.

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Organizational Affiliation: 

Diabetes Protein Engineering, Novo Nordisk A/S , Novo Nordisk Park, 2760 Maaloev, Denmark. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
INSULIN A CHAIN	A, C	21	Homo sapiens	Mutation(s): 0  Gene Names: INS
Find proteins for P01308 (Homo sapiens) Go to Gene View: INS Go to UniProtKB:  P01308

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
INSULIN B CHAIN	B, D	29	Homo sapiens	Mutation(s): 0  Gene Names: INS
Find proteins for P01308 (Homo sapiens) Go to Gene View: INS Go to UniProtKB:  P01308

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	B, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	B, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
IPH	A, C	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N
16E	B	N-(16-Carboxyhexadecanoyl)-L-glutamic acid C21 H37 N O7 SGIVALYPXQHYAY-KRWDZBQOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 78.717	α = 90.00
b = 78.717	β = 90.00
c = 40.551	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-23 
• Released Date: 2013-01-09 
• Deposition Author(s): Steensgaard, D.B., Schluckebier, G., Strauss, H.M., Norrman, M., Thomsen, J.K., Friderichsen, A.V., Havelund, S., Jonassen, I.

Revision History 

• Version 1.0: 2013-01-09
  Type: Initial release
• Version 1.1: 2013-01-30
  Type: Database references
• Version 1.2: 2017-07-05
  Type: Data collection