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

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Basic information

Entry
Database: PDB / ID: 9vin
TitleTernary complex of TNFR1-DD, TRADD-DD and RIPK1-DD
Components
  • Receptor-interacting serine/threonine-protein kinase 1
  • Tumor necrosis factor receptor superfamily member 1A, membrane form
  • Tumor necrosis factor receptor type 1-associated DEATH domain protein
KeywordsAPOPTOSIS / TNFR1 / RIPK1 / TRADD / Death domain
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsLiu, J. / Han, Y. / Zhao, J. / Gao, J. / Yuan, J.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Apr 15, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 2.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Tumor necrosis factor receptor type 1-associated DEATH domain protein
F: Tumor necrosis factor receptor type 1-associated DEATH domain protein
N: Tumor necrosis factor receptor type 1-associated DEATH domain protein
V: Tumor necrosis factor receptor type 1-associated DEATH domain protein
W: Tumor necrosis factor receptor type 1-associated DEATH domain protein
i: Receptor-interacting serine/threonine-protein kinase 1
j: Receptor-interacting serine/threonine-protein kinase 1
k: Receptor-interacting serine/threonine-protein kinase 1
l: Receptor-interacting serine/threonine-protein kinase 1
m: Receptor-interacting serine/threonine-protein kinase 1
n: Receptor-interacting serine/threonine-protein kinase 1
o: Receptor-interacting serine/threonine-protein kinase 1
p: Receptor-interacting serine/threonine-protein kinase 1
q: Receptor-interacting serine/threonine-protein kinase 1
r: Receptor-interacting serine/threonine-protein kinase 1
s: Receptor-interacting serine/threonine-protein kinase 1
t: Receptor-interacting serine/threonine-protein kinase 1
A: Tumor necrosis factor receptor superfamily member 1A, membrane form
B: Tumor necrosis factor receptor superfamily member 1A, membrane form
C: Tumor necrosis factor receptor superfamily member 1A, membrane form
D: Tumor necrosis factor receptor superfamily member 1A, membrane form
G: Tumor necrosis factor receptor superfamily member 1A, membrane form
a: Tumor necrosis factor receptor superfamily member 1A, membrane form
b: Tumor necrosis factor receptor superfamily member 1A, membrane form
c: Tumor necrosis factor receptor superfamily member 1A, membrane form
d: Tumor necrosis factor receptor superfamily member 1A, membrane form
e: Tumor necrosis factor receptor superfamily member 1A, membrane form
f: Tumor necrosis factor receptor superfamily member 1A, membrane form
g: Tumor necrosis factor receptor superfamily member 1A, membrane form
h: Tumor necrosis factor receptor superfamily member 1A, membrane form
u: Receptor-interacting serine/threonine-protein kinase 1


Theoretical massNumber of molelcules
Total (without water)411,67731
Polymers411,67731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Tumor necrosis factor receptor type 1-associated DEATH domain protein / TNFR1-associated DEATH domain protein / TNFRSF1A-associated via death domain


Mass: 13234.913 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRADD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15628
#2: Protein
Receptor-interacting serine/threonine-protein kinase 1 / Cell death protein RIP / Receptor-interacting protein 1 / RIP-1


Mass: 13242.945 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK1, RIP, RIP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q13546, non-specific serine/threonine protein kinase
#3: Protein
Tumor necrosis factor receptor superfamily member 1A, membrane form


Mass: 13334.171 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF1A, TNFAR, TNFR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19438
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
Buffer solutionpH: 7.5
Details: 100 mM NaCl, 20 mM Tris-HCl pH7.5, 1mM EDTA, 1mM DTT.
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
220 mMTris (hydroxymethyl) aminomethane hydrochlorideTris-HCl1
31 mMEthylenediaminetetraacetic acidEDTA1
41 mMDithiothreitolDTT1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2EPUimage acquisition
4cryoSPARC4.6.2CTF correction
7PHENIX1.20.1model fitting
9cryoSPARC4.6.2initial Euler assignment
10cryoSPARC4.6.2final Euler assignment
11cryoSPARC4.6.2classification
12cryoSPARC4.6.23D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 104838
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68510 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building

3D fitting-ID: 1 / Chain-ID: A / Pdb chain-ID: A / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-ID
16AC5

6ac5

6AC51
21ICH

1ich

1ICH2
36ac0

6ac0

6ac03
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 57.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003124661
ELECTRON MICROSCOPYf_angle_d0.546133210
ELECTRON MICROSCOPYf_chiral_restr0.03583656
ELECTRON MICROSCOPYf_plane_restr0.00514298
ELECTRON MICROSCOPYf_dihedral_angle_d3.90523333

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