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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 / cytoplasmic side of plasma membrane / cellular response to tumor necrosis factor / 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: Zhao, K. / Liu, J.P. / Liu, C. / Yuan, J.Y.
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
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
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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