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- PDB-8zuj: Pentagonal cluster of BAFF-BAFFR ectodomain complex -

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Basic information

Entry
Database: PDB / ID: 8zuj
TitlePentagonal cluster of BAFF-BAFFR ectodomain complex
Components
  • Tumor necrosis factor ligand superfamily member 13b, soluble form
  • Tumor necrosis factor receptor superfamily member 13C
KeywordsIMMUNE SYSTEM / BAFF receptor / Receptor / Receptor cluster
Function / homology
Function and homology information


B cell costimulation / positive regulation of germinal center formation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / tumor necrosis factor receptor binding / germinal center formation / skin development / B cell homeostasis / B cell proliferation ...B cell costimulation / positive regulation of germinal center formation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / tumor necrosis factor receptor binding / germinal center formation / skin development / B cell homeostasis / B cell proliferation / T cell proliferation / T cell costimulation / positive regulation of B cell proliferation / positive regulation of T cell proliferation / TNFR2 non-canonical NF-kB pathway / cytokine activity / tumor necrosis factor-mediated signaling pathway / signaling receptor activity / adaptive immune response / receptor ligand activity / signaling receptor binding / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / Tumor necrosis factor receptor 13C/17 / : / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 13C / Tumor necrosis factor ligand superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsLim, C.S. / Lee, J.O.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: Highly ordered clustering of TNFα and BAFF ligand-receptor-intracellular adaptor complexes on a lipid membrane.
Authors: Chan Seok Lim / Jisun Lee / Ji Won Kim / Jie-Oh Lee /
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 ...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.
History
DepositionJun 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 13C
B: Tumor necrosis factor receptor superfamily member 13C
C: Tumor necrosis factor receptor superfamily member 13C
D: Tumor necrosis factor ligand superfamily member 13b, soluble form
E: Tumor necrosis factor ligand superfamily member 13b, soluble form
F: Tumor necrosis factor ligand superfamily member 13b, soluble form
G: Tumor necrosis factor receptor superfamily member 13C
H: Tumor necrosis factor receptor superfamily member 13C
I: Tumor necrosis factor receptor superfamily member 13C
J: Tumor necrosis factor ligand superfamily member 13b, soluble form
K: Tumor necrosis factor ligand superfamily member 13b, soluble form
L: Tumor necrosis factor ligand superfamily member 13b, soluble form
M: Tumor necrosis factor receptor superfamily member 13C
N: Tumor necrosis factor receptor superfamily member 13C
O: Tumor necrosis factor receptor superfamily member 13C
P: Tumor necrosis factor ligand superfamily member 13b, soluble form
Q: Tumor necrosis factor ligand superfamily member 13b, soluble form
R: Tumor necrosis factor ligand superfamily member 13b, soluble form
S: Tumor necrosis factor receptor superfamily member 13C
T: Tumor necrosis factor receptor superfamily member 13C
U: Tumor necrosis factor receptor superfamily member 13C
V: Tumor necrosis factor ligand superfamily member 13b, soluble form
W: Tumor necrosis factor ligand superfamily member 13b, soluble form
X: Tumor necrosis factor ligand superfamily member 13b, soluble form
Y: Tumor necrosis factor receptor superfamily member 13C
Z: Tumor necrosis factor receptor superfamily member 13C
a: Tumor necrosis factor receptor superfamily member 13C
b: Tumor necrosis factor ligand superfamily member 13b, soluble form
c: Tumor necrosis factor ligand superfamily member 13b, soluble form
d: Tumor necrosis factor ligand superfamily member 13b, soluble form


Theoretical massNumber of molelcules
Total (without water)419,81530
Polymers419,81530
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Tumor necrosis factor receptor superfamily member 13C / B-cell-activating factor receptor / BAFF receptor / BAFF-R / BLyS receptor 3


Mass: 10585.881 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF13C, BAFFR, BR3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96RJ3
#2: Protein
Tumor necrosis factor ligand superfamily member 13b, soluble form


Mass: 17401.756 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TNFSF13B, BAFF, BLYS, TALL1, TNFSF20, ZTNF4, UNQ401/PRO738
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y275
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2150 mMSodium chlorideNaCl1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 100500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220800 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 4V46

4v46


Accession code: 4V46 / Source name: PDB / Type: experimental model

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