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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 / 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)
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: Zhao, K. / Liu, J.P. / Liu, C. / Yuan, J.Y.
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
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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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