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- EMDB-65047: Helical assembly of TRADD death domain -

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Basic information

Entry
Database: EMDB / ID: EMD-65047
TitleHelical assembly of TRADD death domain
Map data
Sample
  • Complex: Helical assembly of TRADD death domain protein
    • Protein or peptide: Tumor necrosis factor receptor type 1-associated DEATH domain protein
KeywordsDeath domain / Inflammation / Tumor necrosis factor / APOPTOSIS
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu J / Han Y
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 13, 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_65047.png

Downloads & links

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Map

FileDownload / File: emd_65047.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 270.08 Å		1.06 Å/pix.
x 256 pix.
= 270.08 Å		1.06 Å/pix.
x 256 pix.
= 270.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.21630752 - 0.6683202
Average (Standard dev.)0.006484221 (±0.043721024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65047_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65047_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical assembly of TRADD death domain protein

EntireName: Helical assembly of TRADD death domain protein
Components
  • Complex: Helical assembly of TRADD death domain protein
    • Protein or peptide: Tumor necrosis factor receptor type 1-associated DEATH domain protein

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Supramolecule #1: Helical assembly of TRADD death domain protein

SupramoleculeName: Helical assembly of TRADD death domain protein / 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: 28 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.936616 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AQTFLFQGQP VVNRPLSLKD QQTFARSVGL KWRKVGRSLQ RGCRALRDPA LDSLAYEYER EGLYEQAFQL LRRFVQAEGR RATLQRLVE ALEENELTSL AEDLLGLTDP NGGLA

UniProtKB: Tumor necrosis factor receptor type 1-associated DEATH domain protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / 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
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 5.19 Å
Applied symmetry - Helical parameters - Δ&Phi: 138.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 203507
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 233004 / Software - Name: cryoSPARC (ver. 4.3)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ac0

Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ac0


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9vgd:
Helical assembly of TRADD death domain

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