7K7G: Nucleosome and Gal4 complex
nucleosome and Gal4 complex. Determined by electron microscopy at 4.2 Å resolution. Released 31 Mar 2021.
- Method
- Electron microscopy
- Resolution
- 4.2 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae
- Chains
- 11
- Atoms
- 11,098
- Mol. weight
- 206.63 kDa
- Ligands
- ZN
- Released
- 31 Mar 2021
Explore 7K7G in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7K7G contains 33 α-helices and 18 β-strands across 9 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 and E: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-77 | 13 | |
| β-strand | 84-85 | 2 | 1 |
| α-helix | 87-114 | 28 | |
| β-strand | 119-120 | 2 | 2 |
| α-helix | 122-131 | 10 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-29 | 4 | |
| α-helix | 32-42 | 11 | |
| β-strand | 46-47 | 2 | 2 |
| α-helix | 50-76 | 27 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 84-94 | 11 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-23 | 4 | |
| α-helix | 29-37 | 9 | |
| β-strand | 44-45 | 2 | 4 |
| α-helix | 49-74 | 26 | |
| β-strand | 79-80 | 2 | 5 |
| α-helix | 82-89 | 8 | |
| α-helix | 93-98 | 6 | |
| β-strand | 103 | 1 | 6 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-52 | 11 | |
| β-strand | 57-58 | 2 | 5 |
| α-helix | 60-87 | 28 | |
| β-strand | 92-93 | 2 | 4 |
| α-helix | 95-105 | 11 | |
| α-helix | 109-126 | 18 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-29 | 4 | |
| α-helix | 32-42 | 11 | |
| β-strand | 46-47 | 2 | 8 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 7 |
| α-helix | 84-94 | 11 | |
| β-strand | 98 | 1 | 6 |
Chain G: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-23 | 5 | |
| α-helix | 29-37 | 9 | |
| β-strand | 44-45 | 2 | 9 |
| α-helix | 49-73 | 25 | |
| α-helix | 82-91 | 10 | |
| β-strand | 102-103 | 2 | 3 |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-52 | 11 | |
| α-helix | 60-87 | 28 | |
| β-strand | 92-93 | 2 | 9 |
| α-helix | 95-105 | 11 | |
| α-helix | 109-126 | 18 | |
Chain M: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-19 | 5 | |
| α-helix | 39-42 | 4 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3 | A, E | protein | 136 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P61830 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P02309 (AlphaFold model) |
| Histone H2A.1 | C, G | protein | 132 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P04911 (AlphaFold model) |
| Histone H2B.1 | D, H | protein | 131 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P02293 (AlphaFold model) |
| DNA (147-mer) | I | DNA | 147 | Saccharomyces cerevisiae | |
| DNA (147-mer) | J | DNA | 147 | Saccharomyces cerevisiae | |
| Centromere DNA-binding protein complex CBF3 subunit B | M | protein | 48 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40969 |
Sequence of entity 1 (A, E), FASTA
>7K7G_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS
Sequence of entity 2 (B, F), FASTA
>7K7G_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7K7G_3 Histone H2A.1 (chains C, G)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKATKASQEL
Sequence of entity 4 (D, H), FASTA
>7K7G_4 Histone H2B.1 (chains D, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 5 (I), FASTA
>7K7G_5 DNA (147-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAATATTAGTGTATTTGATTTCCGAAAGTTAA
AAAAGAAATAGTAAGAAATCATCCGAT
Sequence of entity 6 (J), FASTA
>7K7G_6 DNA (147-MER) (chains J)
ATCGGATGATTTCTTACTATTTCTTTTTTAACTTTCGGAAATCAAATACACTAATATTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 7 (M), FASTA
>7K7G_7 Centromere DNA-binding protein complex CBF3 subunit B (chains M)
MFNRTTQLKSKHPCSVCTRRKVKCDRMIPCGNCRKRGQDSECMKSTKL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation. Guan, R., Lian, T., Zhou, B.R. et al. Nat Commun (2021) 12:1763-1763. DOI 10.1038/s41467-021-21985-9 · PubMed
Other PDB entries of the same protein (UniProt P61830 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6KMJ 1.4 Å, Crystal structure of Sth1 bromodomain in complex with H3K14Ac
- 7F3S 1.4 Å, Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide
- 3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
- 8I3F 1.62 Å, Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal
- 2H2G 1.63 Å, The Structural Basis of Sirtuin substrate affinity
- 7F4E 1.78 Å, Crystal structure of Hst2 in complex with H3K9bz peptide
- 5D7E 1.9 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9ac
- 7F4A 2.0 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide
- 1M1D 2.2 Å, Tetrahymena GCN5 with bound bisubstrate analog inhibitor
- 1QSN 2.2 Å, Crystal structure of tetrahymena GCN5 with bound coenzyme a and histone H3 peptide
- 2IDC 2.2 Å, Structure of the Histone H3-Asf1 Chaperone Interaction
- 5IOK 2.22 Å, Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr
Browse structure collections
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