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- EMDB-65094: Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD -

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Basic information

Entry
Database: EMDB / ID: EMD-65094
TitleTernary complex of TNFR1-DD, TRADD-DD and RIPK1-DD
Map data
Sample
  • Complex: Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD
    • Protein or peptide: Tumor necrosis factor receptor type 1-associated DEATH domain protein
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 1A, membrane form
KeywordsTNFR1 / RIPK1 / TRADD / Death domain / APOPTOSIS
Function / homology
Function and homology information


: / pulmonary valve development / tumor necrosis factor receptor superfamily complex / ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / death domain binding / aortic valve development / ripoptosome assembly involved in necroptotic process / negative regulation of extracellular matrix constituent secretion ...: / pulmonary valve development / tumor necrosis factor receptor superfamily complex / ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / death domain binding / aortic valve development / ripoptosome assembly involved in necroptotic process / negative regulation of extracellular matrix constituent secretion / tumor necrosis factor receptor activity / : / positive regulation of apoptotic process involved in morphogenesis / peptidyl-serine autophosphorylation / TNFs bind their physiological receptors / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / tumor necrosis factor binding / Microbial modulation of RIPK1-mediated regulated necrosis / ripoptosome / positive regulation of hair follicle development / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / negative regulation of cardiac muscle hypertrophy / programmed necrotic cell death / TNF signaling / SARS-CoV-1-mediated effects on programmed cell death / Caspase activation via Death Receptors in the presence of ligand / T cell apoptotic process / positive regulation of macrophage differentiation / JUN kinase kinase kinase activity / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / regulation of establishment of endothelial barrier / RIP-mediated NFkB activation via ZBP1 / death-inducing signaling complex / positive regulation of necroptotic process / transmembrane receptor protein tyrosine kinase adaptor activity / negative regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of programmed cell death / positive regulation of programmed necrotic cell death / TNFR1-induced proapoptotic signaling / TNFR1-mediated ceramide production / positive regulation of extrinsic apoptotic signaling pathway / RIPK1-mediated regulated necrosis / prostaglandin metabolic process / positive regulation of lipid metabolic process / TRP channels / Interleukin-10 signaling / necroptotic process / response to tumor necrosis factor / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of execution phase of apoptosis / cell surface receptor signaling pathway via JAK-STAT / extrinsic apoptotic signaling pathway / canonical NF-kappaB signal transduction / signaling adaptor activity / positive regulation of interferon-beta production / TICAM1, RIP1-mediated IKK complex recruitment / tumor necrosis factor-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / : / positive regulation of interleukin-8 production / IKK complex recruitment mediated by RIP1 / protein catabolic process / protein serine/threonine kinase binding / 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 / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein phosphorylation / positive regulation of JNK cascade / Regulation of necroptotic cell death / cellular response to growth factor stimulus / negative regulation of inflammatory response / cellular response to tumor necrosis factor / cytoplasmic side of plasma membrane / positive regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage / kinase binding / cellular response to hydrogen peroxide / cytokine-mediated signaling pathway / positive regulation of tumor necrosis factor production / protein polyubiquitination / positive regulation of inflammatory response / Ovarian tumor domain proteases / protein autophosphorylation / positive regulation of neuron apoptotic process / signaling receptor activity / response to oxidative stress / transcription by RNA polymerase II
Similarity search - Function
TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / RIP1, Death domain / TNFR/NGFR family cysteine-rich region domain profile. ...TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / RIP1, 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 1A / Receptor-interacting serine/threonine-protein kinase 1 / Tumor necrosis factor receptor type 1-associated DEATH domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsLiu J / Han Y / Zhao J / Gao J / Yuan J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
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
DepositionJun 18, 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_65094.png

Downloads & links

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Map

FileDownload / File: emd_65094.map.gz / Format: CCP4 / Size: 103 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.)
1.06 Å/pix.
x 300 pix.
= 316.5 Å		1.06 Å/pix.
x 300 pix.
= 316.5 Å		1.06 Å/pix.
x 300 pix.
= 316.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.393
Minimum - Maximum-0.42042994 - 1.2317266
Average (Standard dev.)0.0033180222 (±0.041607082)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 316.49997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_65094_additional_1.map
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Half map: #2

Fileemd_65094_half_map_1.map
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Half map: #1

Fileemd_65094_half_map_2.map
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Sample components

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Entire : Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD

EntireName: Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD
Components
  • Complex: Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD
    • Protein or peptide: Tumor necrosis factor receptor type 1-associated DEATH domain protein
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 1
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 1A, membrane form

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Supramolecule #1: Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD

SupramoleculeName: Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Tumor necrosis factor receptor type 1-associated DEATH domain protein

MacromoleculeName: Tumor necrosis factor receptor type 1-associated DEATH domain protein
type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.234913 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPGSAQTFLF QGQPVVNRPL SLKDQQTFAR SVGLKWRKVG RSLQRGCRAL RDPALDSLAY EYEREGLYEQ AFQLLRRFVQ AEGRRATLQ RLVEALEENE LTSLAEDLLG LTDPNGGLA

UniProtKB: Tumor necrosis factor receptor type 1-associated DEATH domain protein

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Macromolecule #2: Receptor-interacting serine/threonine-protein kinase 1

MacromoleculeName: Receptor-interacting serine/threonine-protein kinase 1
type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.242945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPGSTNTNFK EEPAAKYQAI FDNTTSLTDK HLDPIRENLG KHWKNCARKL GFTQSQIDEI DHDYERDGLK EKVYQMLQKW VMREGIKGA TVGKLAQALH QCSRIDLLSS LIYVSQN

UniProtKB: Receptor-interacting serine/threonine-protein kinase 1

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Macromolecule #3: Tumor necrosis factor receptor superfamily member 1A, membrane form

MacromoleculeName: Tumor necrosis factor receptor superfamily member 1A, membrane form
type: protein_or_peptide / ID: 3 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.334171 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPGSEDSAHK PQSLDTDDPA TLYAVVENVP PLRWKEFVRR LGLSDHEIDR LELQNGRCLR EAQYSMLATW RRRTPRREAT LELLGRVLR DMDLLGCLED IEEALCGPAA LPPAPSLLR

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

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMTris-HClTris (hydroxymethyl) aminomethane hydrochloride
1.0 mMEDTAEthylenediaminetetraacetic acid
1.0 mMDTTDithiothreitol

Details: 100 mM NaCl, 20 mM Tris-HCl pH7.5, 1mM EDTA, 1mM DTT.
GridModel: Quantifoil / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (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: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 104838
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ac0


Details: 6AC0
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 68510
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6ac5

chain_id: A, source_name: PDB, initial_model_type: experimental model

1ich

chain_id: A, source_name: PDB, initial_model_type: experimental model

6ac0

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9vin:
Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD

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