9R5S: Histone H3.2

Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Determined by electron microscopy at 3.8 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: synthetic construct, Xenopus laevis, Saccharomyces cerevisiae
Chains: 11
Atoms: 17,423
Mol. weight: 376.7 kDa
Released: 28 Jan 2026

Explore 9R5S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9R5S contains 68 α-helices and 37 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
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	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	47-73	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	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	88-97	10
α-helix	103-119	17

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	47-56	10
α-helix	64-78	15
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-93	11
β-strand	97-98	2	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	78	1	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	51	1	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	101-119	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
DNA (160-mer)	I	DNA	160	synthetic construct
DNA (160-mer)	J	DNA	160	synthetic construct
Histone H3.2	A, E	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	C, G	protein	130	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	126	Xenopus laevis	P02281 (AlphaFold model)
Chromo domain-containing protein 1	W	protein	1467	Saccharomyces cerevisiae	P32657

Sequence of entity 1 (I), FASTA

>9R5S_1 DNA (160-MER) (chains I)
CCCTATACGCGGGCGCACTGCAGAAGCTTGGTCCCGGGGCCGCTCAATTGGTCGTAGCAA
GCTCTAGATCCGCTTAATCGAACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGA
TTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATC

Sequence of entity 2 (J), FASTA

>9R5S_2 DNA (160-MER) (chains J)
GATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACG
CGGGGGACAGCGCGTACGTTCGATTAAGCGGATCTAGAGCTTGCTACGACCAATTGAGCG
GCCCCGGGACCAAGCTTCTGCAGTGCGCCCGCGTATAGGG

Sequence of entity 3 (A, E), FASTA

>9R5S_3 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 4 (B, F), FASTA

>9R5S_4 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (C, G), FASTA

>9R5S_5 Histone H2A type 1 (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKK
TESAKSAKSK

Sequence of entity 6 (D, H), FASTA

>9R5S_6 Histone H2B 1.1 (chains D, H)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 7 (W), FASTA

>9R5S_7 Chromo domain-containing protein 1 (chains W)
AAKDISTEVLQNPELYGLRRSHRAAAHQQNYFNDSDDEDDEDNIKQSRRKRMTTIEDDED
EFEDEEGEEDSGEDEDEEDFEEDDDYYGSPIKQNRSKPKSRTKSKSKSKPKSQSEKQSTV
KIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGIDI
VINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKR
LDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDG
TSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRF
EKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFA
RRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKK
TMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLIT
GTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKD
VEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNH
PYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMV
RMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLM
TADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILEY
AIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDLNLDDVLNHAEDH
VTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEYVKEQL
EMMNRRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEVRALYKA
ILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLEKH
ATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSRVEDLK
YLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIRDD
PFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGRRVDYLL
SFLRGGLNTKSPSADIGSKKLPTGPSKKRQRKPANHSKSMTPEITSSEPANGPPSKRMKA
LPKGPAALINNTRLSPNSPTPPLKSKVSRDNGTRQSSNPSSGSAHEKEYDSMDEEDCRHT
MSAIRTSLKRLRRGGKSLDRKEWAKILKTELTTIGNHIESQKGSSRKASPEKYRKHLWSY
SANFWPADVKSTKLMAMYDKITESQKK

Primary citation

Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Hughes, A.L., Sundaramoorthy, R., Owen-Hughes, T. Elife (2025) 14. DOI 10.7554/eLife.52513 · 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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