8IHM: Eaf3 CHD domain
Eaf3 CHD domain bound to the nucleosome. Determined by electron microscopy at 3.58 Å resolution. Released 20 Mar 2024.
- Method
- Electron microscopy
- Resolution
- 3.58 Å
- Organisms
- Xenopus laevis, Saccharomyces cerevisiae
- Chains
- 12
- Atoms
- 13,153
- Mol. weight
- 225.81 kDa
- Released
- 20 Mar 2024
Explore 8IHM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8IHM contains 42 α-helices and 28 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.
Chain A: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-52 | 8 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-114 | 29 | |
| β-strand | 119 | 1 | 2 |
| α-helix | 121-129 | 9 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 2 |
| α-helix | 50-76 | 27 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-70 | 25 | |
| α-helix | 71-73 | 3 | |
| β-strand | 78 | 1 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 6 |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 51 | 1 | 5 |
| α-helix | 53-73 | 21 | |
| α-helix | 76-80 | 5 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 89-98 | 10 | |
| α-helix | 102-121 | 20 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-42 | 3 | |
| α-helix | 47-54 | 8 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 8 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 8 |
| α-helix | 49-75 | 27 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-73 | 28 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-94 | 4 | |
| α-helix | 95-97 | 3 | |
| β-strand | 101-102 | 2 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 10 |
| α-helix | 55-80 | 26 | |
| β-strand | 85-86 | 2 | 9 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
1 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 | A, E | protein | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 129 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B | D, H | protein | 122 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (164-mer) | I | DNA | 164 | Xenopus laevis | |
| DNA (165-mer) | J | DNA | 165 | Xenopus laevis | |
| Rco1-ABR | M | protein | 18 | Saccharomyces cerevisiae | Q04779 |
| Chromatin modification-related protein EAF3 | N | protein | 119 | Saccharomyces cerevisiae | Q12432 |
Sequence of entity 1 (A, E), FASTA
>8IHM_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8IHM_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8IHM_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>8IHM_4 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 5 (I), FASTA
>8IHM_5 DNA (164-MER) (chains I)
TCGCCCTTACTGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGAC
AGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGG
ATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTG
Sequence of entity 6 (J), FASTA
>8IHM_6 DNA (165-MER) (chains J)
CAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCAGTAAGGGCGAC
Sequence of entity 7 (M), FASTA
>8IHM_7 Rco1-ABR (chains M)
RRKIITSEGIERSFKNEH
Sequence of entity 8 (N), FASTA
>8IHM_8 Chromatin modification-related protein EAF3 (chains N)
RCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQKLGEDESIPEEII
NGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKKSLLEQQKKKKL
Primary citation
Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme. Zhang, Y., Xu, M., Wang, P. et al. Cell Res (2023) 33:971-974. DOI 10.1038/s41422-023-00884-2 · 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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