7SSA: Pioneer factor Cbf1
Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome. Determined by electron microscopy at 3.2 Å resolution. Released 5 Apr 2023.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organisms
- Xenopus laevis, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
- Chains
- 12
- Atoms
- 12,480
- Mol. weight
- 280.36 kDa
- Released
- 5 Apr 2023
Explore 7SSA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7SSA contains 40 α-helices and 20 β-strands across 10 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: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 47-73 | 27 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 6 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 5 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 4 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-125 | 19 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 47-73 | 27 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-103 | 3 | 3 |
| α-helix | 114-116 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-49 | 9 | |
| β-strand | 56-57 | 2 | 10 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 9 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-126 | 20 | |
2 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 |
|---|
| Histone H3.2 | A, E | protein | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A.1 | C, G | protein | 131 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P04911 (AlphaFold model) |
| Histone H2B.1 | D, H | protein | 130 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P02293 (AlphaFold model) |
| Centromere-binding protein 1 | K, L | protein | 352 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P17106 |
| DNA (137-mer) | I | DNA | 149 | synthetic construct | |
| DNA (137-mer) | J | DNA | 149 | synthetic construct | |
Sequence of entity 1 (A, E), FASTA
>7SSA_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>7SSA_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7SSA_3 Histone H2A.1 (chains C, G)
SGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLA
AEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKK
SAKATKASQEL
Sequence of entity 4 (D, H), FASTA
>7SSA_4 Histone H2B.1 (chains D, H)
SAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQK
SMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRA
VTKYSSSTQA
Sequence of entity 5 (K, L), FASTA
>7SSA_5 Centromere-binding protein 1 (chains K, L)
GSNSLANNNKLSTEDEEIHSARKRGYNEEQNYSEARKKQRDQGLLSQESNDGNIDSALLS
EGATLKGTQSQYESGLTSNKDEKGSDDEDASVAEAAVAATVNYTDLIQGQEDSSDAHTSN
QTNANGEHKDSLNGERAITPSNEGVKPNTSLEGMTSSPMESTQQSKNDMLIPLAEHDRGP
EHQQDDEDNDDADIDLKKDISMQPGRRGRKPTTLATTDEWKKQRKDSHKEVERRRRENIN
TAINVLSDLLPVRESSKAAILACAAEYIQKLKETDEANIEKWTLQKLLSEQNASQLASAN
EKLQEELGNAYKEIEYMKRVLRKEGIEYEDMHTHKKQENERKSTRSDNPHEA
Sequence of entity 6 (I), FASTA
>7SSA_6 DNA (137-MER) (chains I)
ATCGGAGAGGTCACGTGACCAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTA
AACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCC
AGGGACGTCTCAGATATATACATCCTGAT
Sequence of entity 7 (J), FASTA
>7SSA_7 DNA (137-MER) (chains J)
ATCAGGATGTATATATCTGAGACGTCCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTA
AAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATT
GAGCGGCCTGGTCACGTGACCTCTCCGAT
Primary citation
Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions. Donovan, B.T., Chen, H., Eek, P. et al. Mol Cell (2023) 83:1251-1263.e6. DOI 10.1016/j.molcel.2023.03.006 · PubMed
Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
- 3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
- 1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
- 1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
- 4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
- 1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
- 3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
- 3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
- 3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
- 3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
- 6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
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