9LRV: Fission yeast centromeric nucleosome Class 1
Cryo-EM structure of Fission yeast centromeric nucleosome Class 1. Determined by electron microscopy at 2.99 Å resolution. Released 4 Feb 2026.
- Method
- Electron microscopy
- Resolution
- 2.99 Å
- Organism
- Schizosaccharomyces pombe (strain 972 / ATCC 24843)
- Chains
- 10
- Atoms
- 11,645
- Mol. weight
- 197.79 kDa
- Released
- 4 Feb 2026
Explore 9LRV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9LRV contains 37 α-helices and 16 β-strands across 8 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-37 | 12 | |
| α-helix | 45-60 | 16 | |
| β-strand | 70-71 | 2 | 1 |
| α-helix | 73-100 | 28 | |
| β-strand | 105-106 | 2 | 2 |
| α-helix | 108-118 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-42 | 11 | |
| β-strand | 46-47 | 2 | 2 |
| α-helix | 50-76 | 27 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 84-93 | 10 | |
| β-strand | 97-99 | 3 | 3 |
Chain C: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| α-helix | 19-22 | 4 | |
| α-helix | 29-37 | 9 | |
| α-helix | 48-74 | 27 | |
| β-strand | 79-80 | 2 | 4 |
| α-helix | 82-90 | 9 | |
| α-helix | 93-98 | 6 | |
| β-strand | 103-104 | 2 | 5 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 4 |
| α-helix | 56-83 | 28 | |
| α-helix | 91-101 | 11 | |
| α-helix | 105-121 | 17 | |
Chain E: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-23 | 3 | |
| α-helix | 26-37 | 12 | |
| α-helix | 45-61 | 17 | |
| α-helix | 68-69 | 2 | |
| β-strand | 70-71 | 2 | 6 |
| α-helix | 73-100 | 28 | |
| β-strand | 105-106 | 2 | 7 |
| α-helix | 108-118 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-29 | 4 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 7 |
| α-helix | 50-76 | 27 | |
| β-strand | 81-82 | 2 | 6 |
| α-helix | 84-92 | 9 | |
| β-strand | 98-99 | 2 | 5 |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-23 | 5 | |
| α-helix | 29-37 | 9 | |
| β-strand | 44-45 | 2 | 8 |
| α-helix | 48-74 | 27 | |
| α-helix | 82-91 | 10 | |
| α-helix | 93-98 | 6 | |
| β-strand | 102-104 | 3 | 3 |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 8 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3-like centromeric protein cnp1 | A | protein | 126 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Q9Y812 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | P09322 (AlphaFold model) |
| Histone H2A-alpha | C, G | protein | 132 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | P04909 (AlphaFold model) |
| Histone H2B-alpha | D, H | protein | 126 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | P04913 (AlphaFold model) |
| Histone H3-like centromeric protein cnp1 | E | protein | 120 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Q9Y812 (AlphaFold model) |
| DNA (144-mer) | I | DNA | 147 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | |
| DNA (144-mer) | J | DNA | 147 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | |
Sequence of entity 1 (A), FASTA
>9LRV_1 Histone H3-like centromeric protein cnp1 (chains A)
HHHHHHMAKKSLMAEPGDPIPRPRKKRYRPGTTALREIRKYQRSTDLLIQRLPFSRIVRE
ISSEFVANFSTDVGLRWQSTALQCLQEAAEAFLVHLFEDTNLCAIHAKRVTIMQRDMQLA
RRIRGA
Sequence of entity 2 (B, F), FASTA
>9LRV_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISALVYEETRAVLK
LFLENVIRDAVTYTEHAKRKTVTSLDVVYSLKRQGRTIYGFGG
Sequence of entity 3 (C, G), FASTA
>9LRV_3 Histone H2A-alpha (chains C, G)
MSGGKSGGKAAVAKSAQSRSAKAGLAFPVGRVHRLLRKGNYAQRVGAGAPVYLAAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGHVTIAQGGVVPNINAHLLPK
TSGRTGKPSQEL
Sequence of entity 4 (D, H), FASTA
>9LRV_4 Histone H2B-alpha (chains D, H)
MSAAEKKPASKAPAGKAPRDTMKSADKKRGKNRKETYSSYIYKVLKQVHPDTGISNQAMR
ILNSFVNDIFERIATEASKLAAYNKKSTISSREIQTAVRLILPGELAKHAVTEGTKSVTK
YSSSAQ
Sequence of entity 5 (E), FASTA
>9LRV_5 Histone H3-like centromeric protein cnp1 (chains E)
MAKKSLMAEPGDPIPRPRKKRYRPGTTALREIRKYQRSTDLLIQRLPFSRIVREISSEFV
ANFSTDVGLRWQSTALQCLQEAAEAFLVHLFEDTNLCAIHAKRVTIMQRDMQLARRIRGA
Sequence of entity 6 (I), FASTA
>9LRV_6 DNA (144-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCACATATATACATCCGAT
Sequence of entity 7 (J), FASTA
>9LRV_7 DNA (144-MER) (chains J)
ATCGGATGTATATATGTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Primary citation
Cnp1 N-terminal dynamics regulate L1 loop recognition by Mis15 to orchestrate kinetochore assembly in Schizosaccharomyces pombe. Xiong, Y., Jian, Y., Zhang, Y. et al. J Mol Cell Biol (2026) 18. DOI 10.1093/jmcb/mjaf056 · PubMed
Other PDB entries of the same protein (UniProt Q9Y812 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9LRW 3.04 Å, Cryo-EM structure of Fission yeast centromeric nucleosome Class 2
Browse structure collections
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