7U23 | pdb_00007u23

Single-chain LCDV-1 viral insulin-like peptide bound to IGF-1R ectodomain, leucine-zippered form

• PDB DOI: https://doi.org/10.2210/pdb7U23/pdb
• EM Map EMD-26306: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Lymphocystis disease virus 1
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-02-22 Released: 2022-11-16 
• Deposition Author(s): Kirk, N.S., Lawrence, M.C.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Interaction of a viral insulin-like peptide with the IGF-1 receptor produces a natural antagonist.

Moreau, F., Kirk, N.S., Zhang, F., Gelfanov, V., List, E.O., Chrudinova, M., Venugopal, H., Lawrence, M.C., Jimenez, V., Bosch, F., Kopchick, J.J., DiMarchi, R.D., Altindis, E., Ronald Kahn, C.

(2022) Nat Commun 13: 6700-6700

• PubMed: 36335114 
• DOI: https://doi.org/10.1038/s41467-022-34391-6
• Primary Citation Related Structures: 
  7U23


• PubMed Abstract: 
  

  Lymphocystis disease virus-1 (LCDV-1) and several other Iridoviridae encode viral insulin/IGF-1 like peptides (VILPs) with high homology to human insulin and IGFs. Here we show that while single-chain (sc) and double-chain (dc) LCDV1-VILPs have very low affinity for the insulin receptor, scLCDV1-VILP has high affinity for IGF1R where it can antagonize human IGF-1 signaling, without altering insulin signaling. Consequently, scLCDV1-VILP inhibits IGF-1 induced cell proliferation and growth hormone/IGF-1 induced growth of mice in vivo. Cryo-electron microscopy reveals that scLCDV1-VILP engages IGF1R in a unique manner, inducing changes in IGF1R conformation that led to separation, rather than juxtaposition, of the transmembrane segments and hence inactivation of the receptor. Thus, scLCDV1-VILP is a natural peptide with specific antagonist properties on IGF1R signaling and may provide a new tool to guide development of hormonal analogues to treat cancers or metabolic disorders sensitive to IGF-1 without affecting glucose metabolism.

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Organizational Affiliation: 
• Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA.
WEHI, Parkville, VIC, Australia.
Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia.
Department of Chemistry, Indiana University, Bloomington, IN, USA.
Novo Nordisk, Indianapolis Research Center, Indianapolis, USA.
Edison Biotechnology Institute and Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA.
Boston College Biology Department, Chestnut Hill, MA, USA.
Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia.
Department of Biochemistry and Molecular Biology, School of Veterinary Medicine and Center of Animal Biotechnology and Gene Therapy, Universitat Autonoma de Barcelona, Bellaterra, Spain.
CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), 28029, Madrid, Spain.
Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 231.33 kDa 
• Atom Count: 11,688 
• Modeled Residue Count: 1,462 
• Deposited Residue Count: 2,028 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor 1 receptor	A [auth E], B [auth F]	952	Homo sapiens	Mutation(s): 0  Gene Names: IGF1R EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08069 (Homo sapiens) Explore P08069  Go to UniProtKB:  P08069
PHAROS:  P08069 GTEx:  ENSG00000140443

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
single-chain LCDV-1 viral insulin-like peptide	C, D	62	Lymphocystis disease virus 1	Mutation(s): 0
UniProt
Find proteins for A0A9X9ZA31 (Fish lymphocystis disease virus) Explore A0A9X9ZA31  Go to UniProtKB:  A0A9X9ZA31

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Kirk, N.S., Lawrence, M.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK031036
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	K01DK11796

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.2: 2025-06-04
  Changes: Data collection