9ZDL | pdb_00009zdl

A6-A11 diselenide glargine insulin

  • Classification: HORMONE
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2025-11-25 Released: 2026-08-05 
  • Deposition Author(s): Yang, Y., Dhayalan, B., Ehnbom, A., Weiss, M.A.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

Validation slider image for 9ZDL

This is version 1.0 of the entry. See complete history

Literature

Damping amyloid-associated conformational fluctuations in a protein by an engineered diselenide bridge.

Yang, Y.Dhayalan, B.Ehnbom, A.Weil-Ktorza, O.Metanis, N.Weiss, M.A.

(2026) Protein Sci 35: e70697-e70697

  • DOI: https://doi.org/10.1002/pro.70697
  • Primary Citation Related Structures: 
    9ZDL

  • PubMed Abstract: 

    Polypeptide cross-β assembly, characteristic of diverse proteotoxic diseases, defines a general thermodynamic ground state and limits the shelf lives of peptide- and protein therapeutics. A model is provided by insulin. Although the hormone contains a predominance of α-helix, its fibrils exhibit cross-β reorganization. In the real world, aggregation-coupled fibrillation of insulin underlies its degradation above room temperature, impairing activity and imposing a complex global "cold chain" of transport and storage. Here, we describe biophysical protection of an insulin analog at an elevated temperature by an engineered diselenide bridge. Our studies focused on insulin glargine, the active ingredient of long-acting formulations in broad clinical use. Insoluble in a subcutaneous depot due to its shifted isoelectric point, the analog dissolves at pH 4.0 and so, unlike neutral formulations of the wild-type hormone, is unprotected by zinc-mediated hexamer assembly. Whereas at 37°C the fibrillation lag time of insulin glargine is accelerated by fourfold relative to WT insulin, such instability is circumvented by pairwise substitution of Cys A6 and Cys A11 by selenocysteine. Protection from fibrillation correlates with augmented resistance to pepsin cleavage, guanidine denaturation, and thermal unfolding. Although NMR structures of insulin glargine and its diselenide analog are similar, damping of conformational fluctuations is evidenced by patterns of 1 H-NMR chemical shifts, helix-associated NOEs, amide-resonance line widths, and 1 H- 2 H amide-proton exchange. Such damping is discussed in relation to molecular dynamics simulations. Demonstrating a likely mechanistic relationship between fibrillation and native-state conformational fluctuations, our findings highlight the translational promise of "dynamic engineering" via nonstandard mutagenesis.


  • Organizational Affiliation
    • Department of Biochemistry, Molecular Biology & Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA.

Macromolecule Content 

  • Total Structure Weight: 6.17 kDa 
  • Atom Count: 423 
  • Modeled Residue Count: 53 
  • Deposited Residue Count: 53 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin A chain21Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
GTEx:  ENSG00000254647 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin A chain32Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
GTEx:  ENSG00000254647 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01 DK04949

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-05
    Type: Initial release