9D20 | pdb_00009d20

Crystal structure of DLK1 in complex with ACVR2B

PDB DOI: https://doi.org/10.2210/pdb9D20/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-08-08 Released: 2025-05-07
Deposition Author(s): Ming, Q., Antfolk, D., Luca, V.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free:
0.242 (Depositor), 0.238 (DCC)
R-Value Work:
0.212 (Depositor), 0.214 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Molecular mechanism of Activin receptor inhibition by DLK1.

Antfolk, D., Ming, Q., Manturova, A., Goebel, E.J., Thompson, T.B., Luca, V.C.

(2025) Nat Commun 16: 5976-5976

PubMed: 40593645 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-60634-3
Primary Citation Related Structures:
9D20

PubMed Abstract:
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.

Organizational Affiliation

Department of Immunology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA.

Macromolecule Content

Total Structure Weight: 41.98 kDa
Atom Count: 2,776
Modeled Residue Count: 346
Deposited Residue Count: 350
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activin receptor type-2B	A [auth E], C [auth A]	94	Homo sapiens	Mutation(s): 0 Gene Names: ACVR2B EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q13705 (Homo sapiens) Explore Q13705 Go to UniProtKB: Q13705
PHAROS: Q13705 GTEx: ENSG00000114739
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13705
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth E] Focus chain C [auth A]	Go to GlyGen: Q13705-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein delta homolog 1	B [auth D], D [auth B]	81	Homo sapiens	Mutation(s): 0 Gene Names: DLK1, DLK
UniProt & NIH Common Fund Data Resources
Find proteins for P80370 (Homo sapiens) Explore P80370 Go to UniProtKB: P80370
PHAROS: P80370 GTEx: ENSG00000185559
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80370
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth D] Focus chain D [auth B]	Go to GlyGen: P80370-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E SDF format, chain F [auth E] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain E MOL2 format, chain F [auth E] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain E mmCIF format, chain F [auth E] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	E, F [auth E], O [auth A], P [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E Focus chain F [auth E] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain E Focus chain F [auth E] Focus chain O [auth A] Focus chain P [auth A]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain T [auth B] MOL2 format, chain K [auth D] MOL2 format, chain T [auth B] mmCIF format, chain K [auth D] mmCIF format, chain T [auth B]	K [auth D], T [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain K [auth D] Focus chain T [auth B] Interactions & Density Focus chain K [auth D] Focus chain T [auth B]
FUC Query on FUC Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain J [auth D] MOL2 format, chain S [auth B] MOL2 format, chain J [auth D] mmCIF format, chain S [auth B] mmCIF format, chain J [auth D]	J [auth D], S [auth B]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain J [auth D] Focus chain S [auth B] Interactions & Density Focus chain J [auth D] Focus chain S [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth E] SDF format, chain I [auth E] SDF format, chain N [auth D] SDF format, chain R [auth A] SDF format, chain U [auth B] MOL2 format, chain H [auth E] MOL2 format, chain I [auth E] MOL2 format, chain N [auth D] MOL2 format, chain R [auth A] MOL2 format, chain U [auth B] mmCIF format, chain H [auth E] mmCIF format, chain I [auth E] mmCIF format, chain N [auth D] mmCIF format, chain R [auth A] mmCIF format, chain U [auth B]	H [auth E], I [auth E], N [auth D], R [auth A], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth E] Focus chain I [auth E] Focus chain N [auth D] Focus chain R [auth A] Focus chain U [auth B] Interactions & Density Focus chain H [auth E] Focus chain I [auth E] Focus chain N [auth D] Focus chain R [auth A] Focus chain U [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth E] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain Q [auth A] MOL2 format, chain G [auth E] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth A] mmCIF format, chain G [auth E] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth A]	G [auth E], L [auth D], M [auth D], Q [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth E] Focus chain L [auth D] Focus chain M [auth D] Focus chain Q [auth A] Interactions & Density Focus chain G [auth E] Focus chain L [auth D] Focus chain M [auth D] Focus chain Q [auth A]