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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 / ripoptosome assembly involved in necroptotic process / aortic valve development / : ...: / 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 / ripoptosome assembly involved in necroptotic process / aortic valve development / : / 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 / Microbial modulation of RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / tumor necrosis factor binding / 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 / TNF signaling / programmed necrotic cell death / 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 / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-mediated ceramide production / RIPK1-mediated regulated necrosis / prostaglandin metabolic process / positive regulation of lipid metabolic process / TRP channels / Interleukin-10 signaling / necroptotic process / extrinsic apoptotic signaling pathway via death domain receptors / response to tumor necrosis factor / positive regulation of execution phase of apoptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / : / IKK complex recruitment mediated by RIP1 / negative regulation of extrinsic apoptotic signaling pathway / protein serine/threonine kinase binding / positive regulation of interleukin-8 production / protein catabolic process / 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 / 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 / cytoplasmic side of plasma membrane / cellular response to tumor necrosis factor / 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: Zhao K / Liu JP / Liu C / Yuan JY
History
DepositionJun 18, 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_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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Others
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

Projections

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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
Projections & Slices
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Histogram

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Half map: #1

Fileemd_65094_half_map_2.map
Projections & Slices
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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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