8ZUI image
Deposition Date 2024-06-09
Release Date 2025-06-11
Last Version Date 2025-07-09
Entry Detail
PDB ID:
8ZUI
Keywords:
Title:
Binary cluster of TNF-TNFR1 ectodomain complex
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.56 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Tumor necrosis factor
Gene (Uniprot):TNF
Chain IDs:A, B, C, G, H, I
Chain Length:170
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Tumor necrosis factor receptor superfamily member 1A, membrane form
Gene (Uniprot):TNFRSF1A
Chain IDs:D, E, F, J, K, L
Chain Length:198
Number of Molecules:6
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Highly ordered clustering of TNF alpha and BAFF ligand-receptor-intracellular adaptor complexes on a lipid membrane.
Nat Commun 16 5551 5551 (2025)
PMID: 40593711 DOI: 10.1038/s41467-025-61271-6

Abstact

The TNF family plays a critical role in immune regulation. Here, we present high-resolution structures of clusters formed by two TNF receptor family proteins, TNFR1 and BAFFR. Using a lipid monolayer method to mimic their membrane-bound state, we observe that the TNFα-TNFR1 complex forms highly ordered clusters of trimers on the lipid membrane. A non-competitive TNFR1 antagonist that inhibits receptor activation disrupted these clusters without blocking ligand binding or receptor trimerization. Furthermore, we find that the BAFF-BAFFR, BAFF-TACI, and BAFF-BCMA receptor-ligand complexes predominantly form pentagonal clusters of trimers on the lipid membrane. Notably, the binding of the intracellular adaptor TRAF3 to the BAFF-BAFFR complex induces a structural transition from a pentagonal to a flat hexagonal cluster. Mutations in BAFF that impair BAFFR activation prevented cluster formation. Our findings demonstrate that ligand binding induces the formation of highly ordered clusters of TNFR1 and BAFFR receptors on the lipid membrane, which is essential for their activation.

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Primary Citation of related structures