9LIP: Native PMEL fibril lamella
The cryo-EM structure of the native PMEL fibril lamella. Determined by electron microscopy at 3.48 Å resolution. Released 24 Dec 2025.
- Method
- Electron microscopy
- Resolution
- 3.48 Å
- Organism
- Homo sapiens
- Chains
- 48
- Atoms
- 16,968
- Mol. weight
- 240.67 kDa
- Released
- 24 Dec 2025
Explore 9LIP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9LIP contains 24 α-helices and 204 β-strands across 48 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, m, u and W: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 238-244 | 7 | 21 |
| β-strand | 257-261 | 5 | 24 |
| β-strand | 268-271 | 4 | 24 |
| β-strand | 275-278 | 4 | 21 |
| β-strand | 287-297 | 11 | 24 |
Chains A and Y: 0 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 68-72 | 5 | 22 |
| β-strand | 76 | 1 | 23 |
| β-strand | 81-88 | 8 | 22 |
Chains b, D, H, L, n, P, v and X: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 476-486 | 11 | 24 |
Chain B: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 149-154 | 6 | 25 |
| β-strand | 159-162 | 4 | 25 |
| β-strand | 167-173 | 7 | 22 |
| β-strand | 181-190 | 10 | 25 |
| β-strand | 199-208 | 10 | 25 |
| β-strand | 209 | 1 | 23 |
| β-strand | 212 | 1 | 26 |
| α-helix | 213-214 | 2 | |
| β-strand | 215-221 | 7 | 27 |
Chains c, E, g, I, M, o and Q: 0 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 68-72 | 5 | 28 |
| β-strand | 76-77 | 2 | 29 |
| β-strand | 81-88 | 8 | 28 |
Chain C: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 237-244 | 8 | 27 |
| α-helix | 250-252 | 3 | |
| β-strand | 257-261 | 5 | 26 |
| β-strand | 268-271 | 4 | 26 |
| β-strand | 275-279 | 5 | 27 |
| β-strand | 287-297 | 11 | 26 |
Chains d and J: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 149-154 | 6 | 30 |
| β-strand | 159-162 | 4 | 30 |
| β-strand | 167-173 | 7 | 28 |
| β-strand | 181-190 | 10 | 30 |
| β-strand | 199-208 | 10 | 30 |
| β-strand | 209-210 | 2 | 29 |
| β-strand | 212 | 1 | 31 |
| α-helix | 213-214 | 2 | |
| β-strand | 215-221 | 7 | 32 |
Chains e, i, q and S: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 238-244 | 7 | 32 |
| α-helix | 250-252 | 3 | |
| β-strand | 257-261 | 5 | 31 |
| β-strand | 268-271 | 4 | 31 |
| β-strand | 275-278 | 4 | 32 |
| β-strand | 287-296 | 10 | 31 |
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 |
|---|
| M-alpha | A, E, I, M, Q, U, Y, c, g, k, o, s | protein | 24 | Homo sapiens | P40967 (AlphaFold model) |
| M-alpha | B, F, J, N, R, V, Z, d, h, l, p, t | protein | 75 | Homo sapiens | P40967 (AlphaFold model) |
| M-alpha | C, G, K, O, S, W, a, e, i, m, q, u | protein | 68 | Homo sapiens | P40967 (AlphaFold model) |
| M-beta | D, H, L, P, T, X, b, f, j, n, r, v | protein | 17 | Homo sapiens | P40967 (AlphaFold model) |
Sequence of entity 1 (A, E, I, M, Q, U, Y, c, g, k, o, s), FASTA
>9LIP_1 M-alpha (chains A, E, I, M, Q, U, Y, c, g, k, o, s)
VSLKVSNDGPTLIGANASFSIALN
Sequence of entity 2 (B, F, J, N, R, V, Z, d, h, l, p, t), FASTA
>9LIP_2 M-alpha (chains B, F, J, N, R, V, Z, d, h, l, p, t)
SFVYVWKTWGQYWQVLGGPVSGLSIGTGRAMLGTHTMEVTVYHRRGSRSYVPLAHSSSAF
TITDQVPFSVSVSQL
Sequence of entity 3 (C, G, K, O, S, W, a, e, i, m, q, u), FASTA
>9LIP_3 M-alpha (chains C, G, K, O, S, W, a, e, i, m, q, u)
HFLRNQPLTFALQLHDPSGYLAEADLSYTWDFGDSSGTLISRALVVTHTYLEPGPVTAQV
VLQAAIPL
Sequence of entity 4 (D, H, L, P, T, X, b, f, j, n, r, v), FASTA
>9LIP_4 M-beta (chains D, H, L, P, T, X, b, f, j, n, r, v)
CVLYRYGSFSVTLDIVQ
Primary citation
Atomic structure and in situ visualization of native PMEL lamellae in melanosomes. Ma, B., Yao, Y., Dong, H. et al. Nat Commun (2025) 16:10300-10300. DOI 10.1038/s41467-025-65221-0 · PubMed
Other PDB entries of the same protein (UniProt P40967 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5EU5 1.54 Å, HLA Class I antigen
- 9JST 1.79 Å, Wild-type native PMEL amyloid - polymorph 1
- 9JSU 1.79 Å, Wild-type native PMEL amyloid - polymorph 2
- 9JSV 1.79 Å, G175S mutant native PMEL amyloid
- 9JSX 1.79 Å, G175S PMEL CAF amyloid - in vitro polymerized
- 1TVB 1.8 Å, Crystal structure of Melanoma Antigen gp100(209-217) Bound to Human Class I MHC HLA-A2
- 1TVH 1.8 Å, Crystal structure of Modified Melanoma Antigen gp100(209-T2M) Bound to Human Class I MHC…
- 3CC5 1.91 Å, H-2Db complex with human gp100
- 9JSW 1.94 Å, Wild-type PMEL CAF amyloid -in vitro polymerized
- 5EU3 1.97 Å, HLA Class I antigen
- 5EU6 2.02 Å, HLA Class I antigen
- 5EU4 2.12 Å, HLA Class I antigen
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