9N6K: Histone H4

2.88 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex with DNA-binding domain. Determined by electron microscopy at 2.9 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Xenopus laevis, Saccharomyces cerevisiae, synthetic construct
Chains: 12
Atoms: 25,958
Mol. weight: 451.58 kDa
Released: 11 Jun 2025

Explore 9N6K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N6K contains 123 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.

Chains A and 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	2
α-helix	86-113	28
β-strand	118-119	2	1
α-helix	121-131	11

Chains B and 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	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: 5 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	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-94	4
β-strand	100-102	3	6

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 G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
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	91-94	4
β-strand	100-102	3	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	102-120	19

Chain K: 50 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	132-134	3
α-helix	143-149	7
β-strand	179-186	8	16
β-strand	212-217	6	16
β-strand	226-228	3	16
α-helix	230-233	4
α-helix	239-245	7
α-helix	246-250	5
α-helix	251-258	8
α-helix	264-282	19
α-helix	283-285	3
β-strand	287-296	10	17
β-strand	304-311	8	17
α-helix	316-318	3
β-strand	320-323	4	17
α-helix	324-330	7
α-helix	332-342	11
α-helix	348-350	3
α-helix	358-363	6
α-helix	378-392	15
β-strand	397-399	3	18
α-helix	401-402	2
α-helix	407-420	14
β-strand	428-431	4	18
α-helix	437-447	11
β-strand	453-456	4	18
α-helix	460-470	11
β-strand	472	1	19
α-helix	480-482	3
β-strand	483	1	19
β-strand	487-490	4	18
α-helix	492-497	6
α-helix	499-503	5
β-strand	507-513	7	18
α-helix	517-519	3
α-helix	524-530	7
β-strand	534-540	7	18
α-helix	549-559	11
α-helix	577-589	13
β-strand	594-595	2	18
α-helix	606-608	3
β-strand	609-616	8	20
α-helix	620-630	11
α-helix	634-638	5
α-helix	651-660	10
α-helix	662-664	3
α-helix	669-676	8
α-helix	684-692	9
α-helix	697-709	13
β-strand	714-718	5	20
α-helix	721-734	14
β-strand	738-741	4	20
α-helix	747-757	11
β-strand	766-770	5	20
β-strand	785-788	4	20
α-helix	795-802	8
β-strand	814-821	8	20
α-helix	826-843	18
α-helix	845-847	3
α-helix	858-872	15
α-helix	913-916	4
β-strand	923-926	4	20
α-helix	938-953	16
α-helix	1012-1024	13
α-helix	1032-1037	6
α-helix	1046-1089	44
α-helix	1104-1112	9
β-strand	1119-1120	2	21
β-strand	1128-1129	2	21
α-helix	1130-1150	21
α-helix	1155-1157	3
α-helix	1177-1189	13
α-helix	1195-1200	6
α-helix	1250-1264	15

Chain L: 39 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	132-134	3
β-strand	179-186	8	11
α-helix	204-208	5
β-strand	212-217	6	11
β-strand	226-228	3	11
α-helix	230-233	4
α-helix	239-258	20
α-helix	264-282	19
α-helix	283-285	3
β-strand	287-296	10	12
β-strand	304-311	8	12
α-helix	316-318	3
β-strand	320-323	4	12
α-helix	324-330	7
α-helix	332-342	11
α-helix	358-362	5
α-helix	378-391	14
β-strand	397-399	3	13
α-helix	401-402	2
α-helix	407-420	14
β-strand	428-431	4	13
α-helix	437-447	11
β-strand	453-455	3	13
α-helix	460-469	10
β-strand	472	1	14
α-helix	481-482	2
β-strand	483	1	14
β-strand	487-490	4	13
α-helix	492-497	6
α-helix	499-502	4
β-strand	507-513	7	13
α-helix	515-519	5
α-helix	524-530	7
β-strand	534-540	7	13
α-helix	549-559	11
α-helix	577-589	13
β-strand	594-595	2	13
α-helix	606-608	3
β-strand	609-616	8	15
α-helix	617-619	3
α-helix	620-630	11
α-helix	634-638	5
α-helix	651-660	10
α-helix	662-664	3
α-helix	669-675	7
α-helix	685-693	9
α-helix	696-709	14
β-strand	714-718	5	15
α-helix	721-734	14
β-strand	738-741	4	15
α-helix	747-757	11
β-strand	766-770	5	15
β-strand	785-788	4	15
α-helix	795-802	8
β-strand	814-821	8	15
α-helix	826-839	14
α-helix	840-844	5
α-helix	865-873	9
β-strand	923-924	2	15
α-helix	932-935	4
α-helix	938-953	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H4	B, F	protein	88	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	110	Xenopus laevis	Q6AZJ8 (AlphaFold model)
Histone H2B	D, H	protein	94	Xenopus laevis	P02281 (AlphaFold model)
Histone H3.2	A, E	protein	97	Xenopus laevis	P84233 (AlphaFold model)
Chromo domain-containing protein 1	K, L	protein	1144	Saccharomyces cerevisiae	P32657
DNA Tracking Strand	I	DNA	162	synthetic construct
DNA Lagging Strand	J	DNA	162	synthetic construct

Sequence of entity 1 (B, F), FASTA

>9N6K_1 Histone H4 (chains B, F)
AKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTE
HAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 2 (C, G), FASTA

>9N6K_2 Histone H2A (chains C, G)
TRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK

Sequence of entity 3 (D, H), FASTA

>9N6K_3 Histone H2B (chains D, H)
TRKESYAIYVYKVLKQVHPDTGISCKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITS
REIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 4 (A, E), FASTA

>9N6K_4 Histone H3.2 (chains A, E)
HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEA
YLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 5 (K, L), FASTA

>9N6K_5 Chromo domain-containing protein 1 (chains K, L)
KIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGIDI
VINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKR
LDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDG
TSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRF
EKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFA
RRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKK
TMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLIT
GTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKD
VEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNH
PYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMV
RMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLM
TADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILEY
AIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKGEDGNGDDVLNHAEDH
VTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEYVKEQL
EMMNRRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEVRALYKA
ILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLEKH
ATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSRVEDLK
YLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIRDD
PFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGRRVDYLL
SFLR

Sequence of entity 6 (I), FASTA

>9N6K_6 DNA Tracking Strand (chains I)
CCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACA
GCTCTAGCAACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGG
ATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCC

Sequence of entity 7 (J), FASTA

>9N6K_7 DNA Lagging Strand (chains J)
GGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAAC
GCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTTGCTAGAGCTGTCTACGACCAATTGAG
CGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGCGAAAAGGG

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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