8ZUK | pdb_00008zuk

Cluster structure of the BAFF-BAFFR-TRAF3 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 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: 1,162.29 kDa 
  • Atom Count: 32,550 
  • Modeled Residue Count: 4,116 
  • Deposited Residue Count: 10,563 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TNF receptor-associated factor 3310Homo sapiensMutation(s): 0 
Gene Names: TRAF3CAP-1CRAF1TRAFAMN
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q13114 (Homo sapiens)
Explore Q13114 
Go to UniProtKB:  Q13114
PHAROS:  Q13114
GTEx:  ENSG00000131323 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13114
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 13C193Homo sapiensMutation(s): 0 
Gene Names: TNFRSF13CBAFFRBR3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RJ3 (Homo sapiens)
Explore Q96RJ3 
Go to UniProtKB:  Q96RJ3
PHAROS:  Q96RJ3
GTEx:  ENSG00000159958 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RJ3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: 2025-07-02
    Changes: Data collection
  • Version 1.2: 2025-08-06
    Changes: Data collection, Database references