8ZUI | pdb_00008zui

Binary cluster of TNF-TNFR1 ectodomain complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8ZUI

This is version 1.1 of the entry. See complete history

Literature

Highly ordered clustering of TNF alpha and BAFF ligand-receptor-intracellular adaptor complexes on a lipid membrane.

Lim, C.S.Lee, J.Kim, J.W.Lee, J.O.

(2025) Nat Commun 16: 5551-5551

  • DOI: https://doi.org/10.1038/s41467-025-61271-6
  • Primary Citation Related Structures: 
    8ZUI, 8ZUJ, 8ZUK

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Life Sciences, POSTECH, Pohang, Gyungbuk, 37673, Korea.

Macromolecule Content 

  • Total Structure Weight: 246.28 kDa 
  • Atom Count: 13,378 
  • Modeled Residue Count: 1,722 
  • Deposited Residue Count: 2,208 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor
A, B, C, G, H
A, B, C, G, H, I
170Homo sapiensMutation(s): 0 
Gene Names: TNFTNFATNFSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
PHAROS:  P01375
GTEx:  ENSG00000232810 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01375
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 1A, membrane form
D, E, F, J, K
D, E, F, J, K, L
198Homo sapiensMutation(s): 0 
Gene Names: TNFRSF1ATNFARTNFR1
UniProt & NIH Common Fund Data Resources
Find proteins for P19438 (Homo sapiens)
Explore P19438 
Go to UniProtKB:  P19438
PHAROS:  P19438
GTEx:  ENSG00000067182 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19438
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection, Database references