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- PDB-9vgd: Helical assembly of TRADD death domain -

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Basic information

Entry
Database: PDB / ID: 9vgd
TitleHelical assembly of TRADD death domain
ComponentsTumor necrosis factor receptor type 1-associated DEATH domain protein
KeywordsAPOPTOSIS / Death domain / Inflammation / Tumor necrosis factor
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily complex / death domain binding / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / positive regulation of hair follicle development / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand ...tumor necrosis factor receptor superfamily complex / death domain binding / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / positive regulation of hair follicle development / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / death-inducing signaling complex / transmembrane receptor protein tyrosine kinase adaptor activity / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / canonical NF-kappaB signal transduction / signaling adaptor activity / positive regulation of interferon-beta production / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / cellular response to tumor necrosis factor / cytoplasmic side of plasma membrane / kinase binding / protein polyubiquitination / positive regulation of inflammatory response / cytoskeleton / protein-macromolecule adaptor activity / positive regulation of canonical NF-kappaB signal transduction / signaling receptor complex / positive regulation of cell migration / positive regulation of apoptotic process / apoptotic process / signal transduction / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / 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 type 1-associated DEATH domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu, J. / Han, Y.
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 13, 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: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Apr 15, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Apr 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
A: Tumor necrosis factor receptor type 1-associated DEATH domain protein
B: Tumor necrosis factor receptor type 1-associated DEATH domain protein
C: Tumor necrosis factor receptor type 1-associated DEATH domain protein
E: Tumor necrosis factor receptor type 1-associated DEATH domain protein
F: Tumor necrosis factor receptor type 1-associated DEATH domain protein
H: Tumor necrosis factor receptor type 1-associated DEATH domain protein
I: Tumor necrosis factor receptor type 1-associated DEATH domain protein
J: Tumor necrosis factor receptor type 1-associated DEATH domain protein
K: Tumor necrosis factor receptor type 1-associated DEATH domain protein
M: Tumor necrosis factor receptor type 1-associated DEATH domain protein
N: Tumor necrosis factor receptor type 1-associated DEATH domain protein
Q: Tumor necrosis factor receptor type 1-associated DEATH domain protein
R: Tumor necrosis factor receptor type 1-associated DEATH domain protein
S: Tumor necrosis factor receptor type 1-associated DEATH domain protein
T: 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
Y: Tumor necrosis factor receptor type 1-associated DEATH domain protein
Z: Tumor necrosis factor receptor type 1-associated DEATH domain protein
b: Tumor necrosis factor receptor type 1-associated DEATH domain protein
c: Tumor necrosis factor receptor type 1-associated DEATH domain protein
e: Tumor necrosis factor receptor type 1-associated DEATH domain protein
f: Tumor necrosis factor receptor type 1-associated DEATH domain protein
g: Tumor necrosis factor receptor type 1-associated DEATH domain protein
h: Tumor necrosis factor receptor type 1-associated DEATH domain protein
j: Tumor necrosis factor receptor type 1-associated DEATH domain protein
k: Tumor necrosis factor receptor type 1-associated DEATH domain protein
l: Tumor necrosis factor receptor type 1-associated DEATH domain protein


Theoretical massNumber of molelcules
Total (without water)362,22528
Polymers362,22528
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: 12936.616 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRADD / Production host: Escherichia coli (E. coli) / References: UniProt: Q15628
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Helical assembly of TRADD death domain protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
220 mMTris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
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 defocus max: 2400 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
2EPUimage acquisition
7PHENIX1.20.1-4487model fitting
9cryoSPARC4.3initial Euler assignment
10cryoSPARC4.1final Euler assignment
11cryoSPARC4.1classification
12cryoSPARC4.33D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 138.4 ° / Axial rise/subunit: 5.19 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 233004
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203507 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 6ac0

6ac0


Pdb chain-ID: A / Accession code: 6ac0 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 83.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003424948
ELECTRON MICROSCOPYf_angle_d0.412533600
ELECTRON MICROSCOPYf_chiral_restr0.03173668
ELECTRON MICROSCOPYf_plane_restr0.00364480
ELECTRON MICROSCOPYf_dihedral_angle_d11.06389716

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