8VMN: H3K4me3 nucleosome

H3K4me3 nucleosome bound to PRC2_AJ1-450. Determined by electron microscopy at 3.5 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, Xenopus laevis
Chains: 10
Atoms: 12,540
Mol. weight: 195.76 kDa
Released: 22 Jan 2025

Explore 8VMN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VMN contains 36 α-helices and 16 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 I: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	46-54	9
α-helix	64-74	11
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain J: 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	50-75	26
β-strand	80-81	2	1
α-helix	83-93	11
β-strand	97-98	2	3

Chain K: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
α-helix	80-87	8
α-helix	91-96	6
β-strand	101-102	2	5

Chain M: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	35-45	11
α-helix	54-80	27
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	102-120	19

Chain O: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-75	12
β-strand	84	1	6
α-helix	86-113	28
α-helix	121-130	10

Chain Q: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
α-helix	50-76	27
β-strand	81	1	6
α-helix	83-92	10
β-strand	97-98	2	5

Chain R: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	7
α-helix	46-72	27
β-strand	77-78	2	8
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	3

Chain S: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-43	9
β-strand	50-51	2	8
α-helix	53-80	28
β-strand	85-86	2	7
α-helix	88-98	11
α-helix	102-120	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (157-mer)	H	DNA	157	Homo sapiens
Histone H3.2	I	protein	136	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	J, Q	protein	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2A	K, R	protein	108	Xenopus laevis	Q6AZJ8 (AlphaFold model)
Histone H2B	M, S	protein	96	Xenopus laevis	A0A8J1LZU9 (AlphaFold model)
Histone H3.2	O	protein	136	Homo sapiens	Q71DI3 (AlphaFold model)
DNA (157-mer)	D	DNA	157	Homo sapiens

Sequence of entity 1 (H), FASTA

>8VMN_1 DNA (157-MER) (chains H)
CAGGATGTATATATCTGAGACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTTAA
ACGCGGGGGACAGCGCGTACGTGCGTTTTAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTGGGCACCGGGATTCTCCAGCCGCCGGCAGC

Sequence of entity 2 (I), FASTA

>8VMN_2 Histone H3.2 (chains I)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 3 (J, Q), FASTA

>8VMN_3 Histone H4 (chains J, Q)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (K, R), FASTA

>8VMN_4 Histone H2A (chains K, R)
AKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAAR
DNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKC

Sequence of entity 5 (M, S), FASTA

>8VMN_5 Histone H2B (chains M, S)
RKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTI
TSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 6 (O), FASTA

>8VMN_6 Histone H3.2 (chains O)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 7 (D), FASTA

>8VMN_7 DNA (157-MER) (chains D)
GCTGCCGGCGGCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTA
GCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTAAACCGCCAAGGGGATTACTC
CCTAGTCTCCAGGCACGTCTCAGATATATACATCCTG

Primary citation

Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications. Cookis, T., Lydecker, A., Sauer, P. et al. Nat Struct Mol Biol (2025) 32:393-404. DOI 10.1038/s41594-024-01452-x · 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

Browse structure collections

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