9VIN: PDB entry 9VIN
Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD. Determined by electron microscopy at 3.41 Å resolution. Released 8 Apr 2026.
- Method
- Electron microscopy
- Resolution
- 3.41 Å
- Organism
- Homo sapiens
- Chains
- 31
- Atoms
- 24,273
- Mol. weight
- 411.68 kDa
- Released
- 8 Apr 2026
Explore 9VIN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9VIN contains 215 α-helices and 46 β-strands across 31 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.
Chain a: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 356-364 | 9 | |
| α-helix | 368-378 | 11 | |
| α-helix | 382-391 | 10 | |
| α-helix | 396-410 | 15 | |
| α-helix | 414-416 | 3 | |
| α-helix | 418-428 | 11 | |
| α-helix | 431-440 | 10 | |
Chain A: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 356-364 | 9 | |
| α-helix | 368-376 | 9 | |
| α-helix | 384-389 | 6 | |
| α-helix | 396-410 | 15 | |
| α-helix | 413-415 | 3 | |
| α-helix | 418-426 | 9 | |
| α-helix | 431-440 | 10 | |
Chains b, D and e: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 356-364 | 9 | |
| α-helix | 368-376 | 9 | |
| α-helix | 382-391 | 10 | |
| α-helix | 396-410 | 15 | |
| α-helix | 413-415 | 3 | |
| α-helix | 418-427 | 10 | |
| α-helix | 431-440 | 10 | |
Chain B: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 356-365 | 10 | |
| α-helix | 368-376 | 9 | |
| α-helix | 382-391 | 10 | |
| α-helix | 397-410 | 14 | |
| α-helix | 413-415 | 3 | |
| α-helix | 418-427 | 10 | |
| α-helix | 431-440 | 10 | |
Chain c: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 356-363 | 8 | |
| α-helix | 368-378 | 11 | |
| α-helix | 382-391 | 10 | |
| α-helix | 396-410 | 15 | |
| α-helix | 413-415 | 3 | |
| α-helix | 418-426 | 9 | |
| α-helix | 431-440 | 10 | |
Chain C: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 356-365 | 10 | |
| α-helix | 368-376 | 9 | |
| α-helix | 382-391 | 10 | |
| α-helix | 396-410 | 15 | |
| α-helix | 418-428 | 11 | |
| α-helix | 431-440 | 10 | |
Chain d: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 356-365 | 10 | |
| α-helix | 368-376 | 9 | |
| α-helix | 382-391 | 10 | |
| α-helix | 396-410 | 15 | |
| α-helix | 413-415 | 3 | |
| α-helix | 418-428 | 11 | |
| α-helix | 431-440 | 10 | |
Chain E: 6 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 | 216-223 | 8 | |
| α-helix | 230-237 | 8 | |
| α-helix | 248-255 | 8 | |
| α-helix | 261-276 | 16 | |
| β-strand | 281 | 1 | 2 |
| α-helix | 282-289 | 8 | |
| α-helix | 295-302 | 8 | |
18 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 | E, F, N, V, W | protein | 118 | Homo sapiens | Q15628 (AlphaFold model) |
| Receptor-interacting serine/threonine-protein kinase 1 | i, j, k, l, m, n, o, p, q, r, s, t, u | protein | 116 | Homo sapiens | Q13546 (AlphaFold model) |
| Tumor necrosis factor receptor superfamily member 1A, membrane form | A, B, C, D, G, a, b, c, d, e, f, g, h | protein | 118 | Homo sapiens | P19438 (AlphaFold model) |
Sequence of entity 1 (E, F, N, V, W), FASTA
>9VIN_1 Tumor necrosis factor receptor type 1-associated DEATH domain protein (chains E, F, N, V, W)
GPGSAQTFLFQGQPVVNRPLSLKDQQTFARSVGLKWRKVGRSLQRGCRALRDPALDSLAY
EYEREGLYEQAFQLLRRFVQAEGRRATLQRLVEALEENELTSLAEDLLGLTDPNGGLA
Sequence of entity 2 (i, j, k, l, m, n, o, p, q, r, s, t, u), FASTA
>9VIN_2 Receptor-interacting serine/threonine-protein kinase 1 (chains i, j, k, l, m, n, o, p, q, r, s, t, u)
GPGSTNTNFKEEPAAKYQAIFDNTTSLTDKHLDPIRENLGKHWKNCARKLGFTQSQIDEI
DHDYERDGLKEKVYQMLQKWVMREGIKGATVGKLAQALHQCSRIDLLSSLIYVSQN
Sequence of entity 3 (A, B, C, D, G, a, b, c, d, e, f, g, h), FASTA
>9VIN_3 Tumor necrosis factor receptor superfamily member 1A, membrane form (chains A, B, C, D, G, a, b, c, d, e, f, g, h)
GPGSEDSAHKPQSLDTDDPATLYAVVENVPPLRWKEFVRRLGLSDHEIDRLELQNGRCLR
EAQYSMLATWRRRTPRREATLELLGRVLRDMDLLGCLEDIEEALCGPAALPPAPSLLR
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…
- 9VGD 3.3 Å, Helical assembly of TRADD death domain
- 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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