9Y47: Histone H3.2

Human nucleosome structure on Nickel-NTA lipid affinity grid (C1 refinement). Determined by electron microscopy at 2.74 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 2.74 Å
Organism: Homo sapiens
Chains: 10
Atoms: 11,943
Mol. weight: 229.45 kDa
Released: 29 Oct 2025

Explore 9Y47 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y47 contains 40 α-helices and 18 β-strands across 8 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	45-54	10
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-76	27
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain C: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	4
α-helix	47-72	26
α-helix	80-89	10
α-helix	92-96	5
β-strand	100-102	3	5
α-helix	113-115	3

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	38-48	11
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	105-123	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	6
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	31-41	11
β-strand	45-46	2	7
α-helix	50-75	26
β-strand	80-81	2	6
α-helix	83-92	10
β-strand	96-98	3	5

Chain G: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	17-21	5
α-helix	28-35	8
β-strand	42-43	2	8
α-helix	47-72	26
β-strand	77-78	2	9
α-helix	80-89	10
α-helix	92-96	5
β-strand	100-102	3	3
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	9
α-helix	56-83	28
β-strand	88-89	2	8
α-helix	91-101	11
α-helix	104-123	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	135	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	B, F	protein	102	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1	C, G	protein	163	Homo sapiens	P0C0S8 (AlphaFold model)
Histone H2B type 1-C/E/F/G/I	D, H	protein	125	Homo sapiens	P62807 (AlphaFold model)
Nucleosomal DNA - 185 bp	I	DNA	184	Homo sapiens
Nucleosomal DNA - 185 bp	J	DNA	184	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>9Y47_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9Y47_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9Y47_3 Histone H2A type 1 (chains C, G)
GDYKDDDDKGSSHHHHHHSSGSGGGGGENLYFQGSGRGKQGGKARAKAKTRSSRAGLQFP
VGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLA
IRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>9Y47_4 Histone H2B type 1-C/E/F/G/I (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Sequence of entity 5 (I), FASTA

>9Y47_5 Nucleosomal DNA - 185 bp (chains I)
ATCGCTGTTCAATACATGCTCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGT
AATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGA
GCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAGGGCGGCCGCGTATAG
GGAT

Sequence of entity 6 (J), FASTA

>9Y47_6 Nucleosomal DNA - 185 bp (chains J)
ATCCCTATACGCGGCCGCCCTCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGA
CAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGG
GATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAGCATGTATTGAACAG
CGAT

Primary citation

Nickel-NTA lipid-monolayer affinity grids allow for high-resolution structure determination by cryo-EM. Skrajna, A., Lenger, C., Robinson, E. et al. J Struct Biol (2025) 217:108253-108253. DOI 10.1016/j.jsb.2025.108253 · PubMed

Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

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