6UPH: Yeast Centromeric Nucleosome
Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution. Determined by electron microscopy at 2.7 Å resolution. Released 6 Nov 2019.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), unidentified
- Chains
- 10
- Atoms
- 10,677
- Mol. weight
- 235.1 kDa
- Released
- 6 Nov 2019
Explore 6UPH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6UPH contains 35 α-helices and 20 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 | 137-145 | 9 | |
| α-helix | 155-166 | 12 | |
| β-strand | 177-178 | 2 | 1 |
| α-helix | 180-206 | 27 | |
| β-strand | 212-213 | 2 | 2 |
| α-helix | 215-225 | 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 | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 84-92 | 9 | |
| β-strand | 97-99 | 3 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-89 | 9 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 6 |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-40 | 5 | |
| α-helix | 43-53 | 11 | |
| β-strand | 58-59 | 2 | 5 |
| α-helix | 61-87 | 27 | |
| β-strand | 93-94 | 2 | 4 |
| α-helix | 96-106 | 11 | |
| α-helix | 110-126 | 17 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 134-145 | 12 | |
| α-helix | 155-166 | 12 | |
| β-strand | 177-178 | 2 | 7 |
| α-helix | 180-207 | 28 | |
| β-strand | 212-213 | 2 | 8 |
| α-helix | 215-224 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-40 | 9 | |
| β-strand | 46-47 | 2 | 8 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 7 |
| α-helix | 84-92 | 9 | |
| β-strand | 97-99 | 3 | 6 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 48-71 | 24 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-88 | 8 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 43-53 | 11 | |
| β-strand | 58-59 | 2 | 10 |
| α-helix | 61-88 | 28 | |
| β-strand | 93-94 | 2 | 9 |
| α-helix | 96-106 | 11 | |
| α-helix | 109-126 | 18 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3-like centromeric protein CSE4 | A, E | protein | 229 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P36012 (AlphaFold model) |
| Histone H4 | B, F | protein | 118 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CMU6 (AlphaFold model) |
| Histone H2A | C, G | protein | 145 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CK59 (AlphaFold model) |
| Histone H2B.1 | D, H | protein | 147 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CK60 (AlphaFold model) |
| DNA (119-mer) | I | DNA | 147 | unidentified | |
| DNA (119-mer) | J | DNA | 147 | unidentified | |
Sequence of entity 1 (A, E), FASTA
>6UPH_1 Histone H3-like centromeric protein CSE4 (chains A, E)
MSSKQQWVSSAIQSDSSGRSLSNVNRLAGDQQSINDRALSLLQRTRATKNLFPRREERRR
YESSKSDLDIETDYEDQAGNLEIETENEEEAEMETEVPAPVRTHSYALDRYVRQKRREKQ
RKQSLKRVEKKYTPSELALYEIRKYQRSTDLLISKIPFARLVKEVTDEFTTKDQDLRWQS
MAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARRIRGQFI
Sequence of entity 2 (B, F), FASTA
>6UPH_2 Histone H4 (chains B, F)
HHHHHHENLYFQSNAMSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVK
RISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6UPH_3 Histone H2A (chains C, G)
HHHHHHENLYFQSNAMSGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRKGNYAQRIG
SGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQ
GGVLPNIHQNLLPKKSSKAKASQEL
Sequence of entity 4 (D, H), FASTA
>6UPH_4 Histone H2B.1 (chains D, H)
HHHHHHENLYFQSNAMSAKASKAPASKAPAEKKPAAKKTSSSTDPSKKRTKARKETYSSY
IYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATESSKLAAYNKKSTISAREIQTAVRL
ILPGELAKHAVSEGTRAVTKYSSSTQA
Sequence of entity 5 (I), FASTA
>6UPH_5 DNA (119-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 6 (J), FASTA
>6UPH_6 DNA (119-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Primary citation
Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 angstrom Resolution. Migl, D., Kschonsak, M., Arthur, C.P. et al. Structure (2020) 28:363-370.e3. DOI 10.1016/j.str.2019.12.002 · PubMed
Other PDB entries of the same protein (UniProt P36012 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8T0P 1.73 Å, Structure of Cse4 bound to Ame1 and Okp1
- 7ON1 3.35 Å, Cenp-A nucleosome in complex with Cenp-C
- 8OW0 3.4 Å, Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome
- 8OW1 3.7 Å, Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome.
- 6QLD 4.15 Å, Structure of inner kinetochore CCAN-Cenp-A complex
- 2L5A Structural basis for recognition of centromere specific histone H3 variant by nonhistone…
- 2LY8 The budding yeast chaperone Scm3 recognizes the partially unfolded dimer of the…
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