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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


positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / negative regulation of signaling receptor activity / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / aortic valve development / tumor necrosis factor receptor activity / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of lipid metabolic process / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / negative regulation of extracellular matrix constituent secretion / response to macrophage colony-stimulating factor / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / positive regulation of apoptotic process involved in morphogenesis / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / response to 3,3',5-triiodo-L-thyronine / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / negative regulation of myelination / negative regulation of bicellular tight junction assembly / TNFs bind their physiological receptors / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / tumor necrosis factor binding / : / negative regulation of amyloid-beta clearance / response to isolation stress / positive regulation of action potential / inflammatory response to wounding / positive regulation of interleukin-18 production / death receptor agonist activity / positive regulation of protein transport / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / negative regulation of cardiac muscle hypertrophy / toll-like receptor 3 signaling pathway / embryonic digestive tract development / vascular endothelial growth factor production / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / response to fructose / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / leukocyte tethering or rolling / positive regulation of mononuclear cell migration / positive regulation of fever generation / negative regulation of myoblast differentiation / cellular response to toxic substance / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of D-glucose import / negative regulation of oxidative phosphorylation / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of protein-containing complex disassembly / negative regulation of systemic arterial blood pressure / positive regulation of heterotypic cell-cell adhesion / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage derived foam cell differentiation / regulation of immunoglobulin production / TNFR1-mediated ceramide production / positive regulation of programmed cell death / positive regulation of hepatocyte proliferation / positive regulation of membrane protein ectodomain proteolysis / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of podosome assembly / regulation of canonical NF-kappaB signal transduction / regulation of fat cell differentiation / TNFR1-induced proapoptotic signaling / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of metabolic process / regulation of reactive oxygen species metabolic process / prostaglandin metabolic process / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / response to L-glutamate / negative regulation of fat cell differentiation / regulation of synapse organization / Interleukin-10 signaling / negative regulation of endothelial cell proliferation
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. / TNF(Tumour Necrosis Factor) family ...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. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / 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: To Be Published
Title: Ordered clustering of TNF and BAFF ligand-receptor-adaptor complexes attached to an artificial lipid membrane
Authors: Lim CS / Lee JO
History
DepositionJun 9, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 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
Brightness
Contrast
Others
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60484_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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