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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 / protein localization to plasma membrane / TNFR1-induced NF-kappa-B signaling pathway / 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: Jianping Liu / Jing Zhao / Jiayang Gao / Kun Zhao / Yaoyao Han / Jing Yang / Zefei Li / Jianyu Ye / Ziyu Sun / Fengyi Wang / Xinyi Liu / Zekai Li / Siyu Ji / Bo Liu / Cong Liu / Yixiao Zhang ...Authors: Jianping Liu / Jing Zhao / Jiayang Gao / Kun Zhao / Yaoyao Han / Jing Yang / Zefei Li / Jianyu Ye / Ziyu Sun / Fengyi Wang / Xinyi Liu / Zekai Li / Siyu Ji / Bo Liu / Cong Liu / Yixiao Zhang / Junying Yuan / James J Chou /
Abstract: Dynamic assembly of the complex I signalosome mediated by three death domain (DD)-containing proteins-TNFR1, TRADD and RIPK1-is key for transmitting extracellular TNF stimuli to intracellular NF-κB ...Dynamic assembly of the complex I signalosome mediated by three death domain (DD)-containing proteins-TNFR1, TRADD and RIPK1-is key for transmitting extracellular TNF stimuli to intracellular NF-κB signalling in controlling 'live or die' cell fate. This signalling hub features the rapid recruitment of TRADD and RIPK1 after engagement of TNFR1 by TNF for the formation of complex I, followed by timed disassembly for transition into downstream signalling complexes, but the mechanism driving the dynamic reversibility of complex I remains unclear. Here we captured the assembly core of complex I and determined its cryo-electron microscopy structure, showing a pentameric fibre comprising 31 DDs, with a single layer of a TRADD-DD pentamer sandwiched between multiple layers of TNFR1-DD and RIPK1-DD homopentamers. Structural analysis revealed a strong opposing electric dipole moment (EDM) generated by RIPK1-DD oligomerization relative to that of TNFR1-DD and TRADD-DD. Structure-guided mutagenesis in TNFR1-TRADD-RIPK1 pentameric fibres altering the EDM without affecting DD oligomerization demonstrated the role and mechanism of EDM in driving the dynamic reversibility mediating the rapid assembly and disassembly of complex I. Our study demonstrates a role for long-range interactions mediated by protein EDMs in driving the assembly and disassembly of super-signalling complex I for promoting NF-κB signalling.
History
DepositionMay 30, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 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

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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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
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Half map: #1

Fileemd_64869_half_map_1.map
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Half map: #2

Fileemd_64869_half_map_2.map
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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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