7XVL: Nucleosome-H1.0 Linker Histone Assembly

Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment). Determined by X-ray diffraction at 3.51 Å resolution. Released 24 May 2023.

Method: X-ray diffraction
Resolution: 3.51 Å
Organisms: Homo sapiens, synthetic construct
Chains: 41
Atoms: 52,574
Mol. weight: 882.38 kDa
Released: 24 May 2023

Explore 7XVL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XVL contains 155 α-helices and 84 β-strands across 33 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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	3
α-helix	46-72	27
β-strand	77-78	2	4
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	37
α-helix	107-109	3

Chains A and i: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
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

Chains b and l: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	4
α-helix	56-83	28
β-strand	88-89	2	3
α-helix	91-101	11
α-helix	104-124	21

Chains B and L: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97-98	2	5

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	6
α-helix	46-72	27
β-strand	77-78	2	7
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	8
α-helix	113-115	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	7
α-helix	56-83	28
β-strand	88-89	2	6
α-helix	91-101	11
α-helix	104-123	20

Chain e: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	47-56	10
α-helix	64-76	13
β-strand	83-84	2	11
α-helix	86-113	28
β-strand	118-119	2	12
α-helix	121-131	11

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	9
α-helix	86-113	28
β-strand	118-119	2	10
α-helix	121-131	11

20 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
Histone H3.1	A, E, K, O, U, Y, e, i	protein	138	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F, L, P, V, Z, f, j	protein	105	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G, M, Q, W, a, g, k	protein	132	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-J	D, H, N, R, X, b, h, l	protein	128	Homo sapiens	P06899 (AlphaFold model)
DNA (169-mer)	I, S, c, m	DNA	169	synthetic construct
DNA (169-mer)	J, T, d, n	DNA	169	synthetic construct
Histone H1.0	o	protein	195	Homo sapiens	P07305

Sequence of entity 1 (A, E, K, O, U, Y, e, i), FASTA

>7XVL_1 Histone H3.1 (chains A, E, K, O, U, Y, e, i)
GSMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKS
TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRV
TIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F, L, P, V, Z, f, j), FASTA

>7XVL_2 Histone H4 (chains B, F, L, P, V, Z, f, j)
GSMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGV
LKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G, M, Q, W, a, g, k), FASTA

>7XVL_3 Histone H2A type 1-B/E (chains C, G, M, Q, W, a, g, k)
GSMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEY
LTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP
KKTESHHKAKGK

Sequence of entity 4 (D, H, N, R, X, b, h, l), FASTA

>7XVL_4 Histone H2B type 1-J (chains D, H, N, R, X, b, h, l)
GSMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSK
AMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKA
VTKYTSAK

Sequence of entity 5 (I, S, c, m), FASTA

>7XVL_5 DNA (169-MER) (chains I, S, c, m)
CCAAAAAAAAAACAGCATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGC
ACCGCTTAAACGCACGTACGCGCTGTCTACCGCGTTTTAACCGCCACTAGAAGCGCTTAC
TAGTCTCCAGGCACGTGTGAGACCGGCACATGCAAAAAAAAAACGAGCT

Sequence of entity 6 (J, T, d, n), FASTA

>7XVL_6 DNA (169-MER) (chains J, T, d, n)
CGTTTTTTTTTTGCATGTGCCGGTCTCACACGTGCCTGGAGACTAGTAAGCGCTTCTAGT
GGCGGTTAAAACGCGGTAGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTAC
GACCAATTGAGCGGCCTCGGCACCGGGATGCTGTTTTTTTTTTGGGTAC

Sequence of entity 7 (o), FASTA

>7XVL_7 Histone H1.0 (chains o)
GPTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSHYK
VGENADSQIKLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKVAT
PKKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTVKAKPVKASKPKKAKPV
KPKAKSSAKRAGKKK

Primary citation

Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment). Adhireksan, Z., Sharma, D., Qiuye, B. 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

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