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- EMDB-60485: Pentagonal cluster of BAFF-BAFFR ectodomain complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60485
TitlePentagonal cluster of BAFF-BAFFR ectodomain complex
Map data
Sample
  • Complex: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 13C
    • Protein or peptide: Tumor necrosis factor ligand superfamily member 13b, soluble form
KeywordsBAFF receptor / Receptor / Receptor cluster / IMMUNE SYSTEM
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 / tumor necrosis factor-mediated signaling pathway / positive regulation of B cell proliferation / positive regulation of T cell proliferation / TNFR2 non-canonical NF-kB pathway / cytokine activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 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_60485.png

Downloads & links

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Map

FileDownload / File: emd_60485.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-2.3462617 - 3.429065
Average (Standard dev.)-0.0002033979 (±0.062247124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60485_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_60485_half_map_2.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex

EntireName: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
Components
  • Complex: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 13C
    • Protein or peptide: Tumor necrosis factor ligand superfamily member 13b, soluble form

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Supramolecule #1: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex

SupramoleculeName: Pentagonal cluster of BAFF-BAFFR ectodomain 3:3 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Tumor necrosis factor receptor superfamily member 13C

MacromoleculeName: Tumor necrosis factor receptor superfamily member 13C / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.585881 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
ADPDYKDDDD KRRGPRSLRG RDAPAPTPCV PAECFDLLVR HCVACGLLRT PRPKPAGASS PAPRTALQPQ ESVGAGAGEA ALPLPGLLG GGGSHHHHHH HH

UniProtKB: Tumor necrosis factor receptor superfamily member 13C

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Macromolecule #2: Tumor necrosis factor ligand superfamily member 13b, soluble form

MacromoleculeName: Tumor necrosis factor ligand superfamily member 13b, soluble form
type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.401756 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GSGGSAVQGP EETVTQDCLQ LIADSETPTI QKGSYTFVPW LLSFKRGSAL EEKENKILVK ETGYFFIYGQ VLYTDKTYAM GHLIQRKKV HVFGDELSLV TLFRCIQNMP ETLPNNSCYS AGIAKLEEGD ELQLAIPREN AQISLDGDVT FFGALKLL

UniProtKB: Tumor necrosis factor ligand superfamily member 13B

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 100500
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: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 220800
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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Atomic model buiding 1

Initial modelPDB ID:

4v46


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

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

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