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- PDB-8zuk: Cluster structure of the BAFF-BAFFR-TRAF3 complex -

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Basic information

Entry
Database: PDB / ID: 8zuk
TitleCluster structure of the BAFF-BAFFR-TRAF3 complex
Components
  • TNF receptor-associated factor 3
  • Tumor necrosis factor receptor superfamily member 13C
KeywordsIMMUNE SYSTEM / Receptor cluster / Signal complex / membrane receptor
Function / homology
Function and homology information


B cell costimulation / regulation of interferon-beta production / TRAF3 deficiency - HSE / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / serine/threonine protein kinase complex / thioesterase binding ...B cell costimulation / regulation of interferon-beta production / TRAF3 deficiency - HSE / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / serine/threonine protein kinase complex / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / type I interferon-mediated signaling pathway / regulation of proteolysis / positive regulation of type I interferon production / ubiquitin ligase complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / T cell costimulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of B cell proliferation / signaling adaptor activity / positive regulation of T cell proliferation / regulation of cytokine production / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / tumor necrosis factor-mediated signaling pathway / RING-type E3 ubiquitin transferase / SARS-CoV-1 activates/modulates innate immune responses / cytoplasmic side of plasma membrane / Ovarian tumor domain proteases / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / signaling receptor activity / TRAF3-dependent IRF activation pathway / protein phosphatase binding / regulation of apoptotic process / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / endosome membrane / endosome / external side of plasma membrane / ubiquitin protein ligase binding / apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / mitochondrion / zinc ion binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / Tumor necrosis factor receptor 13C/17 / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa ...Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / Tumor necrosis factor receptor 13C/17 / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
TNF receptor-associated factor 3 / Tumor necrosis factor receptor superfamily member 13C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 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: FSC / Data content type: FSC / 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 1.1Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name
Revision 1.2Aug 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: TNF receptor-associated factor 3
B: TNF receptor-associated factor 3
C: TNF receptor-associated factor 3
D: Tumor necrosis factor receptor superfamily member 13C
E: Tumor necrosis factor receptor superfamily member 13C
F: Tumor necrosis factor receptor superfamily member 13C
G: TNF receptor-associated factor 3
H: TNF receptor-associated factor 3
I: TNF receptor-associated factor 3
J: Tumor necrosis factor receptor superfamily member 13C
K: Tumor necrosis factor receptor superfamily member 13C
L: Tumor necrosis factor receptor superfamily member 13C
M: TNF receptor-associated factor 3
N: TNF receptor-associated factor 3
O: TNF receptor-associated factor 3
P: Tumor necrosis factor receptor superfamily member 13C
Q: Tumor necrosis factor receptor superfamily member 13C
R: Tumor necrosis factor receptor superfamily member 13C
S: TNF receptor-associated factor 3
T: TNF receptor-associated factor 3
U: TNF receptor-associated factor 3
V: Tumor necrosis factor receptor superfamily member 13C
W: Tumor necrosis factor receptor superfamily member 13C
X: Tumor necrosis factor receptor superfamily member 13C
Y: TNF receptor-associated factor 3
Z: TNF receptor-associated factor 3
a: TNF receptor-associated factor 3
b: Tumor necrosis factor receptor superfamily member 13C
c: Tumor necrosis factor receptor superfamily member 13C
d: Tumor necrosis factor receptor superfamily member 13C
e: TNF receptor-associated factor 3
f: TNF receptor-associated factor 3
g: TNF receptor-associated factor 3
h: Tumor necrosis factor receptor superfamily member 13C
i: Tumor necrosis factor receptor superfamily member 13C
j: Tumor necrosis factor receptor superfamily member 13C
k: TNF receptor-associated factor 3
l: TNF receptor-associated factor 3
m: TNF receptor-associated factor 3
n: Tumor necrosis factor receptor superfamily member 13C
o: Tumor necrosis factor receptor superfamily member 13C
p: Tumor necrosis factor receptor superfamily member 13C


Theoretical massNumber of molelcules
Total (without water)1,162,29242
Polymers1,162,29242
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 ...
TNF receptor-associated factor 3 / CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein ...CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein 1 / LAP1 / RING-type E3 ubiquitin transferase TRAF3


Mass: 35444.441 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF3, CAP-1, CRAF1, TRAFAMN / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q13114, RING-type E3 ubiquitin transferase
#2: Protein ...
Tumor necrosis factor receptor superfamily member 13C / B-cell-activating factor receptor / BAFF receptor / BAFF-R / BLyS receptor 3


Mass: 19902.789 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF13C, BAFFR, BR3 / Cell line (production host): HEK293s GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q96RJ3
Has protein modificationN

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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: Cluster structure of the BAFF-BAFFR-TRAF3 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205165 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18T5P

8t5p

18T5P1PDBexperimental model
22GKW

2gkw

12GKW2PDBexperimental model
RefinementCross valid method: NONE

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