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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


: / tumor necrosis factor receptor superfamily complex / pulmonary valve development / response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of fractalkine production ...: / tumor necrosis factor receptor superfamily complex / pulmonary valve development / response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of fractalkine production / positive regulation of blood microparticle formation / aortic valve development / positive regulation of chronic inflammatory response to antigenic stimulus / negative regulation of extracellular matrix constituent secretion / tumor necrosis factor receptor activity / response to 3,3',5-triiodo-L-thyronine / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of protein transport / positive regulation of vitamin D biosynthetic process / positive regulation of apoptotic process involved in morphogenesis / positive regulation of translational initiation by iron / : / chronic inflammatory response to antigenic stimulus / regulation of endothelial cell apoptotic process / response to macrophage colony-stimulating factor / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / response to gold nanoparticle / negative regulation of myelination / TNFs bind their physiological receptors / positive regulation of JUN kinase activity / tumor necrosis factor binding / negative regulation of vascular wound healing / negative regulation of cytokine production involved in immune response / negative regulation of amyloid-beta clearance / positive regulation of hair follicle development / negative regulation of cardiac muscle hypertrophy / death receptor agonist activity / inflammatory response to wounding / positive regulation of action potential / positive regulation of interleukin-18 production / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / vascular endothelial growth factor production / negative regulation of D-glucose import across plasma membrane / leukocyte migration involved in inflammatory response / embryonic digestive tract development / positive regulation of fever generation / response to fructose / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / necroptotic signaling pathway / leukocyte tethering or rolling / positive regulation of mononuclear cell migration / positive regulation of hepatocyte proliferation / negative regulation of myoblast differentiation / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / regulation of metabolic process / negative regulation of oxidative phosphorylation / positive regulation of protein-containing complex disassembly / positive regulation of protein localization to cell surface / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of osteoclast differentiation / cellular response to toxic substance / positive regulation of heterotypic cell-cell adhesion / macrophage activation involved in immune response / tumor necrosis factor receptor binding / negative regulation of systemic arterial blood pressure / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / negative regulation of mitotic cell cycle / regulation of immunoglobulin production / positive regulation of podosome assembly / positive regulation of chemokine (C-X-C motif) ligand 2 production / regulation of fat cell differentiation / positive regulation of programmed cell death / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / response to L-glutamate / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of neuroinflammatory response / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / TNFR1-mediated ceramide production / positive regulation of DNA biosynthetic process / regulation of reactive oxygen species metabolic process / prostaglandin metabolic process / negative regulation of heart rate / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / negative regulation of bicellular tight junction assembly / positive regulation of lipid metabolic process / response to isolation stress / negative regulation of fat cell differentiation / regulation of synapse organization / negative regulation of endothelial cell proliferation / Interleukin-10 signaling
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. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / 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

Size
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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

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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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Density Histograms

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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