9N6I: Histone H4

2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex. Determined by electron microscopy at 2.61 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.61 Å
Organisms: synthetic construct, Xenopus laevis, Saccharomyces cerevisiae
Chains: 12
Atoms: 24,520
Mol. weight: 375.57 kDa
Released: 11 Jun 2025

Explore 9N6I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N6I contains 113 α-helices and 66 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	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	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	93-96	4
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	45-54	10
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: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
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

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
DNA Tracking Strand	I	DNA	151	synthetic construct
DNA Lagging Strand	J	DNA	151	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)
Histone H3	A, E	protein	100	Xenopus laevis	A0A310TTQ1 (AlphaFold model)
Chromo domain-containing protein 1	K, L	protein	835	Saccharomyces cerevisiae	P32657

Sequence of entity 1 (I), FASTA

>9N6I_1 DNA Tracking Strand (chains I)
GCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCAAC
CGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTTCCTA
GTCTCCAGGCACGTGTCAGATATATACATCC

Sequence of entity 2 (J), FASTA

>9N6I_2 DNA Lagging Strand (chains J)
GGATGTATATATCTGACACGTGCCTGGAGACTAGGAAGTAATCCCCTTGGCGGTTAAAAC
GCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTTGCTAGAGCTGTCTACGACCAATTGAG
CGGCCTCGGCACCGGGATTCTCCAGGGCGGC

Sequence of entity 3 (B, F), FASTA

>9N6I_3 Histone H4 (chains B, F)
AKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTE
HAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>9N6I_4 Histone H2A (chains C, G)
TRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK

Sequence of entity 5 (D, H), FASTA

>9N6I_5 Histone H2B 1.1 (chains D, H)
TRKESYAIYVYKVLKQVHPDTGISCKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITS
REIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 6 (A, E), FASTA

>9N6I_6 Histone H3 (chains A, E)
KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEA
SEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 7 (K, L), FASTA

>9N6I_7 Chromo domain-containing protein 1 (chains K, L)
KIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGIDI
VINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKR
LDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDG
TSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRF
EKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFA
RRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKK
TMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLIT
GTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKD
VEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNH
PYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMV
RMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLM
TADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILEY
AIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKGEDGNGDDVLNHAEDH
VTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEY

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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