9D20 image
Deposition Date 2024-08-08
Release Date 2025-05-07
Last Version Date 2025-07-16
Entry Detail
PDB ID:
9D20
Title:
Crystal structure of DLK1 in complex with ACVR2B
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.67 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein delta homolog 1
Gene (Uniprot):DLK1
Chain IDs:B (auth: D), D (auth: B)
Chain Length:81
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Activin receptor type-2B
Gene (Uniprot):ACVR2B
Chain IDs:A (auth: E), C (auth: A)
Chain Length:94
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Molecular mechanism of Activin receptor inhibition by DLK1.
Nat Commun 16 5976 5976 (2025)
PMID: 40593645 DOI: 10.1038/s41467-025-60634-3

Abstact

Delta-like non-canonical Notch ligand 1 (DLK1) influences myogenesis, adipogenesis, and other aspects of human development through a process that is largely attributed to the downregulation of Notch signaling. Here, we show that DLK1 does not bind to Notch receptors or affect ligand-mediated Notch activation, but instead engages the TGF-β superfamily member Activin receptor type 2B (ACVR2B). The crystal structure of the DLK1-ACVR2B complex reveals that DLK1 mimics the binding mode of canonical TGF-β ligands to compete for access to ACVR2B. In functional assays, DLK1 antagonizes Myostatin-ACVR2B signaling to promote myoblast differentiation, rationalizing a mechanism for the role of DLK1 in muscle development and regeneration. Crosstalk between Notch and TGF-β is mediated by interactions between the transcriptional regulators SMAD2/3 and the Notch intracellular domain (NICD), and DLK1 inhibits SMAD2/3-NICD colocalization. These findings indicate that DLK1 acts directly on ACVR2B to inhibit signaling, whereas the observed effects on Notch may be an indirect result of DLK1 interference with NICD-SMAD complex formation.

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