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- EMDB-60484: Binary cluster of TNF-TNFR1 ectodomain complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60484
TitleBinary cluster of TNF-TNFR1 ectodomain complex
Map data
Sample
  • Complex: Binary cluster of TNF-TNFR1 ectodomain 3:3 complex
    • Protein or peptide: Tumor necrosis factor
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 1A, membrane form
KeywordsTNF receptor / Receptor / Receptor cluster / IMMUNE SYSTEM
Function / homology
Function and homology information


pulmonary valve development / tumor necrosis factor receptor superfamily complex / response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / response to quercetin / negative regulation of branching involved in lung morphogenesis / positive regulation of fractalkine production ...pulmonary valve development / tumor necrosis factor receptor superfamily complex / response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / response to quercetin / negative regulation of branching involved in lung morphogenesis / positive regulation of fractalkine production / positive regulation of blood microparticle formation / aortic valve development / response to 3,3',5-triiodo-L-thyronine / negative regulation of extracellular matrix constituent secretion / tumor necrosis factor receptor activity / positive regulation of protein transport / positive regulation of vitamin D biosynthetic process / chronic inflammatory response to antigenic stimulus / positive regulation of apoptotic process involved in morphogenesis / regulation of endothelial cell apoptotic process / endothelial cell apoptotic process / response to macrophage colony-stimulating factor / negative regulation of myelination / positive regulation of leukocyte adhesion to arterial endothelial cell / response to gold nanoparticle / TNFs bind their physiological receptors / negative regulation of vascular wound healing / Differentiation of naive CD4+ T cells to T helper 1 cells (Th1 cells) / negative regulation of cytokine production involved in immune response / tumor necrosis factor binding / negative regulation of amyloid-beta clearance / positive regulation of podosome assembly / response to resveratrol / positive regulation of hair follicle development / inflammatory response to wounding / positive regulation of interleukin-18 production / positive regulation of hepatocyte proliferation / activation of NF-kappaB-inducing kinase activity / positive regulation of action potential / toll-like receptor 3 signaling pathway / TNF signaling / embryonic digestive tract development / negative regulation of D-glucose import across plasma membrane / vascular endothelial growth factor production / negative regulation of cardiac muscle hypertrophy / positive regulation of fever generation / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of protein localization to cell surface / response to fructose / negative regulation of mitotic cell cycle / leukocyte tethering or rolling / necroptotic signaling pathway / positive regulation of synoviocyte proliferation / regulation of establishment of endothelial barrier / positive regulation of mononuclear cell migration / negative regulation of oxidative phosphorylation / macrophage activation involved in immune response / response to hydrogen sulfide / positive regulation of glial cell proliferation / positive regulation of protein-containing complex disassembly / positive regulation of osteoclast differentiation / cellular response to toxic substance / positive regulation of macrophage derived foam cell differentiation / regulation of fat cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / tumor necrosis factor receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of membrane protein ectodomain proteolysis / negative regulation of systemic arterial blood pressure / response to L-glutamate / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / negative regulation of fat cell differentiation / regulation of reactive oxygen species metabolic process / positive regulation of cytokine production involved in inflammatory response / TNFR1-mediated ceramide production / prostaglandin metabolic process / positive regulation of programmed cell death / negative regulation of heart rate / negative regulation of viral genome replication / positive regulation of DNA biosynthetic process / positive regulation of neuroinflammatory response / positive regulation of amyloid-beta formation / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell proliferation / negative regulation of interleukin-6 production / positive regulation of immunoglobulin production / negative regulation of bicellular tight junction assembly / response to isolation stress / Interleukin-10 signaling / regulation of synapse organization / negative regulation of apoptotic signaling pathway / regulation of insulin secretion / histone H3K9ac reader activity / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / response to salt stress / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
Similarity search - Function
Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. ...Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor-like domain superfamily / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor / Tumor necrosis factor receptor superfamily member 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 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-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60484.png

Downloads & links

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Map

FileDownload / File: emd_60484.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.112
Minimum - Maximum-0.001850971 - 2.1539085
Average (Standard dev.)0.0010238572 (±0.023334458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60484_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60484_half_map_2.map
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Sample components

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Entire : Binary cluster of TNF-TNFR1 ectodomain 3:3 complex

EntireName: Binary cluster of TNF-TNFR1 ectodomain 3:3 complex
Components
  • Complex: Binary cluster of TNF-TNFR1 ectodomain 3:3 complex
    • Protein or peptide: Tumor necrosis factor
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 1A, membrane form

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Supramolecule #1: Binary cluster of TNF-TNFR1 ectodomain 3:3 complex

SupramoleculeName: Binary cluster of TNF-TNFR1 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

MacromoleculeName: Tumor necrosis factor / type: protein_or_peptide / ID: 1 / Details: TNF ligand / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.855344 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
ADPVRSSSRT PSDKPVAHVV ANPQAEGQLQ WLNRRANALL ANGVELRDNQ LVVPSEGLYL IYSQVLFKGQ GCPSTHVLLT HTISRIAVS YQTKVNLLSA IKSPCQRETP EGAEAKPWYE PIYLGGVFQL EKGDRLSAEI NRPDYLDFAE SGQVYFGIIA L EFRSGRLV PR

UniProtKB: Tumor necrosis factor

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Macromolecule #2: Tumor necrosis factor receptor superfamily member 1A, membrane form

MacromoleculeName: Tumor necrosis factor receptor superfamily member 1A, membrane form
type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.190912 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ADPLVPHLGD REKRDSVCPQ GKYIHPQNNS ICCTKCHKGT YLYNDCPGPG QDTDCRECES GSFTASENHL RHCLSCSKCR KEMGQVEIS SCTVDRDTVC GCRKNQYRHY WSENLFQCFN CSLCLNGTVH LSCQEKQNTV CTCHAGFFLR ENECVSCSNC K KSLECTKL ...String:
ADPLVPHLGD REKRDSVCPQ GKYIHPQNNS ICCTKCHKGT YLYNDCPGPG QDTDCRECES GSFTASENHL RHCLSCSKCR KEMGQVEIS SCTVDRDTVC GCRKNQYRHY WSENLFQCFN CSLCLNGTVH LSCQEKQNTV CTCHAGFFLR ENECVSCSNC K KSLECTKL CLPQIENVKG TEDSGTTGGG GSHHHHHHHH

UniProtKB: Tumor necrosis factor receptor superfamily member 1A

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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: 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
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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1800466
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7kp7

source_name: PDB, initial_model_type: experimental model

7kpb

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

PDB-8zui:
Binary cluster of TNF-TNFR1 ectodomain complex

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