7XX6: Nucleosome-H1.0 Linker Histone Assembly
Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment). Determined by X-ray diffraction at 3.39 Å resolution. Released 31 May 2023.
- Method
- X-ray diffraction
- Resolution
- 3.39 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 42
- Atoms
- 53,518
- Mol. weight
- 905.44 kDa
- Ligands
- CA
- Released
- 31 May 2023
Explore 7XX6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7XX6 contains 162 α-helices and 89 β-strands across 34 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: 7 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 | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 4 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 39 |
| α-helix | 113-115 | 3 | |
| α-helix | 117-118 | 2 | |
Chains A and U: 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 | |
Chain b: 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, f and V: 4 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 | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 5 |
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 | 6 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 7 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 8 |
| α-helix | 113-115 | 3 | |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-33 | 4 | |
| 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-56 | 10 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 11 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 12 |
| α-helix | 121-131 | 11 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 9 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 10 |
| α-helix | 121-131 | 11 | |
22 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, p | protein | 195 | Homo sapiens | P07305 |
Sequence of entity 1 (A, E, K, O, U, Y, e, i), FASTA
>7XX6_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
>7XX6_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
>7XX6_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
>7XX6_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
>7XX6_5 DNA (169-MER) (chains I, S, c, m)
GCTTTTTTTTTTCACAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGC
ACCGCTTAAACGCACGTACGGAATCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTAC
GACCAATTGAGCGGCCTCGGCACCGGGATTGTGAAAAAAAAAAGCTGCA
Sequence of entity 6 (J, T, d, n), FASTA
>7XX6_6 DNA (169-MER) (chains J, T, d, n)
GCTTTTTTTTTTCACAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGC
ACCGCTTAAACGCACGTACGGATTCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTAC
GACCAATTGAGCGGCCTCGGCACCGGGATTGTGAAAAAAAAAAGCTGCA
Sequence of entity 7 (o, p), FASTA
>7XX6_7 Histone H1.0 (chains o, p)
GPTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSHYK
VGENADSQIKLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKVAT
PKKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTVKAKPVKASKPKKAKPV
KPKAKSSAKRAGKKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 47 |
Water and common crystallization additives (K) are not listed.
Primary citation
Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment). Adhireksan, Z., Qiuye, B., Lee, P.L. 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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