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- EMDB-64869: Cryo-EM structure of human TNFR1 DD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-64869
TitleCryo-EM structure of human TNFR1 DD filament
Map data
Sample
  • Organelle or cellular component: TNFR1 DD filament
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 1A, membrane form
KeywordsDeath doamin / PROTEIN FIBRIL
Function / homology
Function and homology information


: / pulmonary valve development / tumor necrosis factor receptor superfamily complex / aortic valve development / : / negative regulation of extracellular matrix constituent secretion / tumor necrosis factor receptor activity / positive regulation of apoptotic process involved in morphogenesis / TNFs bind their physiological receptors / tumor necrosis factor binding ...: / pulmonary valve development / tumor necrosis factor receptor superfamily complex / aortic valve development / : / negative regulation of extracellular matrix constituent secretion / tumor necrosis factor receptor activity / positive regulation of apoptotic process involved in morphogenesis / TNFs bind their physiological receptors / tumor necrosis factor binding / negative regulation of cardiac muscle hypertrophy / TNF signaling / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-induced proapoptotic signaling / TNFR1-mediated ceramide production / prostaglandin metabolic process / positive regulation of lipid metabolic process / Interleukin-10 signaling / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / cell surface receptor signaling pathway via JAK-STAT / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / negative regulation of canonical NF-kappaB signal transduction / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / negative regulation of inflammatory response / intrinsic apoptotic signaling pathway in response to DNA damage / cytokine-mediated signaling pathway / protein polyubiquitination / positive regulation of inflammatory response / signaling receptor activity / transcription by RNA polymerase II / positive regulation of canonical NF-kappaB signal transduction / signaling receptor complex / defense response to bacterium / membrane raft / inflammatory response / Golgi membrane / cell surface / positive regulation of transcription by RNA polymerase II / : / extracellular region / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. ...Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / 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 receptor superfamily member 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsZhao K / Liu JP / Liu C / Yuan JY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2026
Title: Electric dipole moment drives the dynamics of the TNFR1 complex I signalosome
Authors: Zhao K / Liu JP / Liu C / Yuan JY
History
DepositionMay 30, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64869.png

Downloads & links

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Map

FileDownload / File: emd_64869.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.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.09588697 - 0.15343668
Average (Standard dev.)0.00015457113 (±0.004289698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64869_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64869_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64869_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TNFR1 DD filament

EntireName: TNFR1 DD filament
Components
  • Organelle or cellular component: TNFR1 DD filament
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 1A, membrane form

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Supramolecule #1: TNFR1 DD filament

SupramoleculeName: TNFR1 DD filament / type: organelle_or_cellular_component / 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 1A, membrane form

MacromoleculeName: Tumor necrosis factor receptor superfamily member 1A, membrane form
type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.035875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EDSAHKPQSL DTDDPATLYA VVENVPPLRW KEFVRRLGLS DHEIDRLELQ NGRCLREAQY SMLATWRRRT PRREATLELL GRVLRDMDL LGCLEDIEEA LCGPAALPPA PSLLR

UniProtKB: Tumor necrosis factor receptor superfamily member 1A

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.30557 Å
Applied symmetry - Helical parameters - Δ&Phi: 138.364 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 512379
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1ich

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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