8PI5

Crystal structure of human insulin desB30 precursor with an Alanine-Methionine-Lysine C-peptide in hexamer (T3R3) conformation

• PDB DOI: https://doi.org/10.2210/pdb8PI5/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2023-06-21 Released: 2023-11-08 
• Deposition Author(s): Johansson, E., Schluckebier, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Molecular engineering of insulin for recombinant expression in yeast.

Kjeldsen, T., Andersen, A.S., Hubalek, F., Johansson, E., Kreiner, F.F., Schluckebier, G., Kurtzhals, P.

(2024) Trends Biotechnol 42: 464-478

• PubMed: 37880066 
• DOI: https://doi.org/10.1016/j.tibtech.2023.09.012
• Primary Citation of Related Structures:  
  8PI4, 8PI5, 8PI6, 8PJC, 8PJH


• PubMed Abstract: 
  

  Since the first administration of insulin to a person with diabetes in 1922, scientific contributions from academia and industry have improved insulin therapy and access. The pharmaceutical need for insulin is now more than 40 tons annually, half of which is produced by recombinant secretory expression in Saccharomyces cerevisiae. We discuss how, in this yeast species, adaptation of insulin precursors by removable structural elements is pivotal for efficient secretory expression. The technologies reviewed have been implemented at industrial scale and are seminal for the supply of human insulin and insulin analogues to people with diabetes now and in the future. Engineering of a target protein with removable structural elements may provide a general approach to yield optimisation.

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Organizational Affiliation: 

Novo Nordisk A/S, Bagsværd, Denmark. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 12.47 kDa 
• Atom Count: 971 
• Modelled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin B chain,Insulin A chain	A [auth B], B [auth D]	53	Homo sapiens	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RCO	H [auth D]	RESORCINOL C6 H6 O2 GHMLBKRAJCXXBS-UHFFFAOYSA-N
ZN	C [auth B], D [auth B], E [auth B], F [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	G [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.353	α = 90
b = 79.353	β = 90
c = 39.185	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Johansson, E., Schluckebier, G.

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Funding Organization	Location	Grant Number
Not funded	Denmark	--

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 1.1: 2024-04-17
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Structure summary