9VGD: Helical assembly of TRADD death domain
Helical assembly of TRADD death domain. Determined by electron microscopy at 3.3 Å resolution. Released 8 Apr 2026.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Homo sapiens
- Chains
- 28
- Atoms
- 24,584
- Mol. weight
- 362.23 kDa
- Released
- 8 Apr 2026
Explore 9VGD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9VGD contains 241 α-helices and 112 β-strands across 28 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chains A, g, J, Q and R: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 201-204 | 4 | 1 |
| β-strand | 207-210 | 4 | 1 |
| β-strand | 213 | 1 | 2 |
| α-helix | 216-224 | 9 | |
| α-helix | 227-229 | 3 | |
| α-helix | 230-237 | 8 | |
| α-helix | 248-255 | 8 | |
| α-helix | 257-259 | 3 | |
| α-helix | 261-276 | 16 | |
| α-helix | 277-279 | 3 | |
| β-strand | 281 | 1 | 2 |
| α-helix | 282-291 | 10 | |
| α-helix | 295-302 | 8 | |
Chains b, h, M and S: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 201-204 | 4 | 43 |
| β-strand | 207-210 | 4 | 43 |
| β-strand | 213 | 1 | 44 |
| α-helix | 216-224 | 9 | |
| α-helix | 227-229 | 3 | |
| α-helix | 230-238 | 9 | |
| α-helix | 248-255 | 8 | |
| α-helix | 257-259 | 3 | |
| α-helix | 261-276 | 16 | |
| α-helix | 277-279 | 3 | |
| β-strand | 281 | 1 | 44 |
| α-helix | 282-291 | 10 | |
| α-helix | 295-302 | 8 | |
Chain B: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 201-204 | 4 | 5 |
| β-strand | 207-210 | 4 | 5 |
| β-strand | 213 | 1 | 6 |
| α-helix | 216-225 | 10 | |
| α-helix | 227-229 | 3 | |
| α-helix | 230-237 | 8 | |
| α-helix | 248-255 | 8 | |
| α-helix | 257-259 | 3 | |
| α-helix | 261-276 | 16 | |
| α-helix | 277-279 | 3 | |
| β-strand | 281 | 1 | 6 |
| α-helix | 282-291 | 10 | |
| α-helix | 295-302 | 8 | |
Chains c, j and N: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 201-204 | 4 | 45 |
| β-strand | 207-210 | 4 | 45 |
| β-strand | 213 | 1 | 46 |
| α-helix | 216-224 | 9 | |
| α-helix | 227-229 | 3 | |
| α-helix | 230-237 | 8 | |
| α-helix | 248-255 | 8 | |
| α-helix | 261-276 | 16 | |
| α-helix | 277-279 | 3 | |
| β-strand | 281 | 1 | 46 |
| α-helix | 282-291 | 10 | |
| α-helix | 295-302 | 8 | |
Chain C: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 201-204 | 4 | 9 |
| β-strand | 207-210 | 4 | 9 |
| β-strand | 213 | 1 | 10 |
| α-helix | 216-223 | 8 | |
| α-helix | 227-229 | 3 | |
| α-helix | 230-238 | 9 | |
| α-helix | 248-255 | 8 | |
| α-helix | 257-259 | 3 | |
| α-helix | 261-276 | 16 | |
| α-helix | 277-279 | 3 | |
| β-strand | 281 | 1 | 10 |
| α-helix | 282-291 | 10 | |
| α-helix | 295-301 | 7 | |
Chain e: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 201-204 | 4 | 47 |
| β-strand | 207-210 | 4 | 47 |
| β-strand | 213 | 1 | 48 |
| α-helix | 216-224 | 9 | |
| α-helix | 227-229 | 3 | |
| α-helix | 230-238 | 9 | |
| α-helix | 248-255 | 8 | |
| α-helix | 261-276 | 16 | |
| α-helix | 277-279 | 3 | |
| β-strand | 281 | 1 | 48 |
| α-helix | 282-291 | 10 | |
| α-helix | 295-302 | 8 | |
Chains E and Z: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 201-204 | 4 | 11 |
| β-strand | 207-210 | 4 | 11 |
| β-strand | 213 | 1 | 12 |
| α-helix | 216-225 | 10 | |
| α-helix | 227-229 | 3 | |
| α-helix | 230-238 | 9 | |
| α-helix | 248-255 | 8 | |
| α-helix | 257-259 | 3 | |
| α-helix | 261-276 | 16 | |
| α-helix | 277-279 | 3 | |
| β-strand | 281 | 1 | 12 |
| α-helix | 282-291 | 10 | |
| α-helix | 295-302 | 8 | |
Chain f: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 201-204 | 4 | 49 |
| β-strand | 207-210 | 4 | 49 |
| β-strand | 213 | 1 | 50 |
| α-helix | 216-225 | 10 | |
| α-helix | 227-229 | 3 | |
| α-helix | 230-237 | 8 | |
| α-helix | 248-255 | 8 | |
| α-helix | 261-276 | 16 | |
| α-helix | 277-279 | 3 | |
| β-strand | 281 | 1 | 50 |
| α-helix | 282-291 | 10 | |
| α-helix | 295-302 | 8 | |
7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Tumor necrosis factor receptor type 1-associated DEATH domain protein | A, B, C, E, F, H, I, J, K, M, N, Q, R, S, T, V, W, Y, Z, b, c, e, f, g, h, j, k, l | protein | 114 | Homo sapiens | Q15628 (AlphaFold model) |
Sequence of entity 1 (A, B, C, E, F, H, I, J, K, M, N, Q, R, S, T, V, W, Y, Z, b, c, e, f, g, h, j, k, l), FASTA
>9VGD_1 Tumor necrosis factor receptor type 1-associated DEATH domain protein (chains A, B, C, E, F, H, I, J, K, M, N, Q, R, S, T, V, W, Y, Z, b, c, e, f, g, h, j, k, l)
AQTFLFQGQPVVNRPLSLKDQQTFARSVGLKWRKVGRSLQRGCRALRDPALDSLAYEYER
EGLYEQAFQLLRRFVQAEGRRATLQRLVEALEENELTSLAEDLLGLTDPNGGLA
Primary citation
Electric dipole moment drives the dynamics of the TNFR1 complex I signalosome. Liu, J., Zhao, J., Gao, J. et al. Nature (2026) 653:1196-1204. DOI 10.1038/s41586-026-10304-1 · PubMed
Other PDB entries of the same protein (UniProt Q15628 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6AC0 1.45 Å, Crystal structure of TRADD death domain GlcNAcylated by EPEC effector NleB
- 1F3V 2.0 Å, Crystal structure of the complex between the N-terminal domain of TRADD and the TRAF…
- 9VIN 3.41 Å, Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD
- 1F2H Solution structure of the N-terminal domain of the TNFR1 associated protein, tradd.
- 5XME Solution structure of C-terminal domain of TRADD
- 7CSQ Solution structure of the complex between p75NTR-DD and TRADD-DD
Browse structure collections
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