9N6H: Histone H4
2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex. Determined by electron microscopy at 2.54 Å resolution. Released 11 Jun 2025.
- Method
- Electron microscopy
- Resolution
- 2.54 Å
- Organisms
- synthetic construct, Xenopus laevis, Saccharomyces cerevisiae
- Chains
- 11
- Atoms
- 18,807
- Mol. weight
- 283.84 kDa
- Released
- 11 Jun 2025
Explore 9N6H in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9N6H contains 81 α-helices and 42 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 | 40-42 | 3 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 2 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 1 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 2 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 117-118 | 2 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-121 | 20 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 8 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 8 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chain G: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-14 | 4 | |
| α-helix | 17-20 | 4 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 113-115 | 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 | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 9 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
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 |
|---|
| DNA Tracking Strand | I | DNA | 160 | synthetic construct | |
| DNA Lagging Strand | J | DNA | 160 | synthetic construct | |
| Histone H4 | B, F | protein | 88 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 110 | Xenopus laevis | Q6AZJ8 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 94 | Xenopus laevis | P02281 (AlphaFold model) |
| Chromo domain-containing protein 1 | K | protein | 835 | Saccharomyces cerevisiae | P32657 (AlphaFold model) |
| Histone H3 | A, E | protein | 98 | Xenopus laevis | A0A310TTQ1 |
Sequence of entity 1 (I), FASTA
>9N6H_1 DNA Tracking Strand (chains I)
CCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCAACC
GCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAG
TCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTA
Sequence of entity 2 (J), FASTA
>9N6H_2 DNA Lagging Strand (chains J)
TACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGG
CGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTTGCTAGAGCTGTCTACG
ACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGG
Sequence of entity 3 (B, F), FASTA
>9N6H_3 Histone H4 (chains B, F)
AKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTE
HAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 4 (C, G), FASTA
>9N6H_4 Histone H2A (chains C, G)
TRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
Sequence of entity 5 (D, H), FASTA
>9N6H_5 Histone H2B 1.1 (chains D, H)
TRKESYAIYVYKVLKQVHPDTGISCKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITS
REIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Sequence of entity 6 (K), FASTA
>9N6H_6 Chromo domain-containing protein 1 (chains K)
KIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGIDI
VINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKR
LDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDG
TSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRF
EKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFA
RRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKK
TMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLIT
GTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKD
VEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNH
PYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMV
RMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLM
TADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILEY
AIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKGEDGNGDDVLNHAEDH
VTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEY
Sequence of entity 7 (A, E), FASTA
>9N6H_7 Histone H3 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Primary citation
A competitive regulatory mechanism of the Chd1 remodeler is integral to distorting nucleosomal DNA. Nodelman, I.M., Folkwein, H.J., Glime, W.S. et al. Nat Struct Mol Biol (2025) 32:1445-1455. DOI 10.1038/s41594-025-01556-y · PubMed
Other PDB entries of the same protein (UniProt P62799 (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
- 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
- 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
- 4ZBJ 2.25 Å, UBN1 peptide bound to H3.3/H4/Asf1
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
- 1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
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