9DJW image
Deposition Date 2024-09-06
Release Date 2025-09-10
Last Version Date 2026-03-25
Entry Detail
PDB ID:
9DJW
Keywords:
Title:
X-ray crystal structure of TNFa-VNAR D1 complex
Biological Source:
Source Organism(s):
Squalus acanthias (Taxon ID: 7797)
Homo sapiens (Taxon ID: 9606)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
3.43 Å
R-Value Free:
0.28
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antigen receptor
Gene (Uniprot):NAR
Chain IDs:A (auth: 0), B (auth: 1), F (auth: 5), G (auth: 6), H (auth: 7), L (auth: D), M (auth: E), N (auth: F), R (auth: J), S (auth: K), T (auth: L), X (auth: P), Y (auth: Q), Z (auth: R), DA (auth: V), EA (auth: W), FA (auth: X), JA (auth: b), KA (auth: c), LA (auth: d), PA (auth: h), QA (auth: i), RA (auth: j), VA (auth: n), WA (auth: o), XA (auth: p), BB (auth: t), CB (auth: u), DB (auth: v), HB (auth: z)
Chain Length:156
Number of Molecules:30
Biological Source:Squalus acanthias
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tumor necrosis factor
Gene (Uniprot):TNF
Chain IDs:C (auth: 2), D (auth: 3), E (auth: 4), I (auth: A), J (auth: B), K (auth: C), O (auth: G), P (auth: H), Q (auth: I), U (auth: M), V (auth: N), W (auth: O), AA (auth: S), BA (auth: T), CA (auth: U), GA (auth: Y), HA (auth: Z), IA (auth: a), MA (auth: e), NA (auth: f), OA (auth: g), SA (auth: k), TA (auth: l), UA (auth: m), YA (auth: q), ZA (auth: r), AB (auth: s), EB (auth: w), FB (auth: x), GB (auth: y)
Chain Length:156
Number of Molecules:30
Biological Source:Homo sapiens
Primary Citation
The structural basis for the selective antagonism of soluble TNF-alpha by shark variable new antigen receptors.
Nat Commun 17 256 256 (2025)
PMID: 41318641 DOI: 10.1038/s41467-025-66967-3

Abstact

The pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-alpha) is synthesized as transmembrane TNF-alpha (tmTNF-alpha) where proteolytic processing releases soluble TNF-alpha (sTNF-alpha). tmTNF-alpha can act as either a ligand by activating TNF receptors, or a receptor that transmits reverse (outside-to-inside) signalling after binding to native receptors. All TNF-alpha therapies bind tmTNF-alpha and induce reverse signalling which can result in immunosuppression leading to infection. We present crystal structures of two anti-TNF-alpha Variable New Antigen Receptors (VNARs) in complex with sTNF-alpha via two distinct epitopes. The VNAR-D1 recognizes an epitope that selectively engages sTNF-alpha while VNAR-C4 binds an epitope that partially overlaps with other biologic therapies. In activated CD4(+) T cells, our VNARs do not induce reverse signalling in contrast to currently available therapies. Our findings suggest that neutralization through a unique mechanism may lead to anti-TNF-alpha agents with an improved safety profile that will benefit high-risk patients.

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Primary Citation of related structures
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