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- EMDB-60486: Cluster structure of the BAFF-BAFFR-TRAF3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60486
TitleCluster structure of the BAFF-BAFFR-TRAF3 complex
Map data
Sample
  • Complex: Cluster structure of the BAFF-BAFFR-TRAF3 complex
    • Protein or peptide: TNF receptor-associated factor 3
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 13C
KeywordsReceptor cluster / Signal complex / membrane receptor / IMMUNE SYSTEM
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 / serine/threonine protein kinase complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / 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 / serine/threonine protein kinase complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / 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 / type I interferon-mediated signaling pathway / regulation of proteolysis / ubiquitin ligase complex / positive regulation of B cell proliferation / T cell costimulation / positive regulation of type I interferon production / signaling adaptor activity / regulation of cytokine production / positive regulation of T cell proliferation / 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 / tumor necrosis factor-mediated signaling pathway / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin-protein transferase activity / Ovarian tumor domain proteases / 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 / endosome membrane / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / mitochondrion / zinc ion binding / identical protein binding / plasma membrane / cytoplasm / cytosol
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsLim CS / Lee JO
Funding support Korea, Republic Of, 1 items
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, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60486.png

Downloads & links

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Map

FileDownload / File: emd_60486.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.222
Minimum - Maximum-0.004323417 - 1.8643266
Average (Standard dev.)0.002063532 (±0.030712537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60486_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60486_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cluster structure of the BAFF-BAFFR-TRAF3 complex

EntireName: Cluster structure of the BAFF-BAFFR-TRAF3 complex
Components
  • Complex: Cluster structure of the BAFF-BAFFR-TRAF3 complex
    • Protein or peptide: TNF receptor-associated factor 3
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 13C

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Supramolecule #1: Cluster structure of the BAFF-BAFFR-TRAF3 complex

SupramoleculeName: Cluster structure of the BAFF-BAFFR-TRAF3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TNF receptor-associated factor 3

MacromoleculeName: TNF receptor-associated factor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.444441 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSNSLEKKVS LLQNESVEKN KSIQSLHNQI CSFEIEIERQ KEMLRNNESK ILHLQRVIDS QAEKLKELDK EIRPFRQNWE EADSMKSSV ESLQNRVTEL ESVDKSAGQV ARNTGLLESQ LSRHDQMLSV HDIRLADMDL RFQVLETASY NGVLIWKIRD Y KRRKQEAV ...String:
MSNSLEKKVS LLQNESVEKN KSIQSLHNQI CSFEIEIERQ KEMLRNNESK ILHLQRVIDS QAEKLKELDK EIRPFRQNWE EADSMKSSV ESLQNRVTEL ESVDKSAGQV ARNTGLLESQ LSRHDQMLSV HDIRLADMDL RFQVLETASY NGVLIWKIRD Y KRRKQEAV MGKTLSLYSQ PFYTGYFGYK MCARVYLNGD GMGKGTHLSL FFVIMRGEYD ALLPWPFKQK VTLMLMDQGS SR RHLGDAF KPDPNSSSFK KPTGEMNIAS GCPVFVAQTV LENGTYIKDD TIFIKVIVDT SDLPDPGGSL VPR

UniProtKB: TNF receptor-associated factor 3

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Macromolecule #2: Tumor necrosis factor receptor superfamily member 13C

MacromoleculeName: Tumor necrosis factor receptor superfamily member 13C / type: protein_or_peptide / ID: 2 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.902789 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ ESVGAGAGEA ALPLPGLLFG APALLGLAL VLALVLVGLV SWRRRQRRLR GASSAEAPDG DKDAPEPLDK VIILSPGISD ATAPAWPPPG EDPGTTPPGH S VPVPATEL ...String:
MRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ ESVGAGAGEA ALPLPGLLFG APALLGLAL VLALVLVGLV SWRRRQRRLR GASSAEAPDG DKDAPEPLDK VIILSPGISD ATAPAWPPPG EDPGTTPPGH S VPVPATEL GSTELVTTKT AGPEQQSNSL EVLFQ

UniProtKB: Tumor necrosis factor receptor superfamily member 13C

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205165
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8t5p

source_name: PDB, initial_model_type: experimental model

2gkw

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

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

PDB-9uje:
Cryo-EM structure of SARS-CoV2 KP.3.1.1 spike protein

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