8VLR: Native H2AK119bu nucleosome at 2.6

Cryo-EM structure of native H2AK119bu nucleosome at 2.6. Determined by electron microscopy at 2.6 Å resolution. Released 15 Jan 2025.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 10
Atoms: 11,657
Mol. weight: 170.58 kDa
Released: 15 Jan 2025

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

Secondary structure: helices and β-sheets

8VLR contains 42 α-helices and 20 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	45-56	12
α-helix	64-73	10
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	82	1
α-helix	83-92	10
β-strand	97-98	2	3

Chain C: 6 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	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	5
α-helix	57-84	28
β-strand	89-90	2	4
α-helix	92-102	11
α-helix	105-124	20

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	82	1
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 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	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	3
α-helix	113-115	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1	A, E	protein	98	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	84	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	108	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-A	D, H	protein	93	Homo sapiens	Q96A08 (AlphaFold model)
DNA (136-mer)	K	DNA	136	Homo sapiens
DNA (136-mer)	L	DNA	136	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>8VLR_1 Histone H3.1 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>8VLR_2 Histone H4 (chains B, F)
RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKR
KTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>8VLR_3 Histone H2A type 1-B/E (chains C, G)
RAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK

Sequence of entity 4 (D, H), FASTA

>8VLR_4 Histone H2B type 1-A (chains D, H)
TRKESYSIYIYKVLKQVHPDTGISSKAMSIMNSFVTDIFERIASEASRLAHYSKRSTISS
REIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS

Sequence of entity 5 (K), FASTA

>8VLR_5 DNA (136-MER) (chains K)
TCTCTGCCTGTTCTTCCAAAAGTGTATTTAGAAACTGCTCCAACAAAAGGCAGGTTCAGC
TGAATTCAGCTGAACCTGCCTTTTGATGGAGCAGTTACCAAATACACTTTTGGTAGAATC
TGGTGCTCCATTATGA

Sequence of entity 6 (L), FASTA

>8VLR_6 DNA (136-MER) (chains L)
TCATAATGGAGCACCAGATTCTACCAAAAGTGTATTTGGTAACTGCTCCATCAAAAGGCA
GGTTCAGCTGAATTCAGCTGAACCTGCCTTTTGTTGGAGCAGTTTCTAAATACACTTTTG
GAAGAACAGGCAGAGA

Primary citation

Role of histone variants H2BC1 and H2AZ.2 in H2AK119ub nucleosome organization and Polycomb gene silencing. Shen, X.Y., Chen, C.X., Wang, Y. et al. To be published.

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

Browse structure collections

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