6LA2: Histone H3.1
343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0. Determined by X-ray diffraction at 3.89 Å resolution. Released 17 Feb 2021.
- Method
- X-ray diffraction
- Resolution
- 3.89 Å
- Organisms
- Homo sapiens, other sequences
- Chains
- 38
- Atoms
- 53,828
- Mol. weight
- 905.03 kDa
- Released
- 17 Feb 2021
Explore 6LA2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6LA2 contains 159 α-helices and 86 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.
Chains a, G and Q: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 23 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 24 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 13 |
| α-helix | 113-115 | 3 | |
Chains A, e, K and U: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 21 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 22 |
| α-helix | 121-131 | 11 | |
Chains b, D and R: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 24 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 23 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-124 | 21 | |
Chains B, F, P, V and Z: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 22 |
| α-helix | 49-75 | 27 | |
| β-strand | 80-81 | 2 | 21 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 25 |
Chains C, M and W: 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 | 26 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 27 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 28 |
| α-helix | 113-115 | 3 | |
Chains E and i: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-39 | 3 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 29 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 30 |
| α-helix | 121-131 | 11 | |
Chain f: 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 | 49-75 | 27 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 82 | 1 | |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 5 |
Chain g: 8 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 | 6 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 7 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 8 |
| α-helix | 113-115 | 3 | |
| α-helix | 117-118 | 2 | |
6 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 | 136 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F, L, P, V, Z, f, j | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G, M, Q, W, a, g, k | protein | 130 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-J | D, H, N, R, X, b, h, l | protein | 126 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (343-mer) | I, c | DNA | 343 | other sequences | |
| DNA (343-mer) | J, d | DNA | 343 | other sequences | |
| Histone H1.0 | S, T | protein | 194 | Homo sapiens | P07305 |
Sequence of entity 1 (A, E, K, O, U, Y, e, i), FASTA
>6LA2_1 Histone H3.1 (chains A, E, K, O, U, Y, e, i)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F, L, P, V, Z, f, j), FASTA
>6LA2_2 Histone H4 (chains B, F, L, P, V, Z, f, j)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G, M, Q, W, a, g, k), FASTA
>6LA2_3 Histone H2A type 1-B/E (chains C, G, M, Q, W, a, g, k)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 4 (D, H, N, R, X, b, h, l), FASTA
>6LA2_4 Histone H2B type 1-J (chains D, H, N, R, X, b, h, l)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (I, c), FASTA
>6LA2_5 DNA (343-MER) (chains I, c)
CGCTGAAAAAAAACGCATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGC
ACCGCTTAAACGCACGTACGCGCTGTCTACCGCGTTTTAACCGCCACTAGAAGCGCTTAC
TAGTCTCCAGGCACGTGTGAGACCGGCACATGAAAAAAAAAAGCATGCTCGAGTATGAAA
AAAAAAACGCATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCTACCGCGTTTTAACCGCCACTAGAAGCGCTTACTAGTCT
CCAGGCACGTGTGAGACCGGCACATGAAAAAAAACAGCGGTAC
Sequence of entity 6 (J, d), FASTA
>6LA2_6 DNA (343-MER) (chains J, d)
CGCTGTTTTTTTTCATGTGCCGGTCTCACACGTGCCTGGAGACTAGTAAGCGCTTCTAGT
GGCGGTTAAAACGCGGTAGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTAC
GACCAATTGAGCGGCCTCGGCACCGGGATGCGTTTTTTTTTTCATACTCGAGCATGCTTT
TTTTTTTCATGTGCCGGTCTCACACGTGCCTGGAGACTAGTAAGCGCTTCTAGTGGCGGT
TAAAACGCGGTAGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGAGCGGCCTCGGCACCGGGATGCGTTTTTTTTCAGCGGTAC
Sequence of entity 7 (S, T), FASTA
>6LA2_7 Histone H1.0 (chains S, T)
MTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSHYKV
GENADSQIKLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKVATP
KKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTVKAKPVKASKPKKAKPVK
PKAKSSAKRAGKKK
Primary citation
Engineering nucleosomes for generating diverse chromatin assemblies. Adhireksan, Z., Sharma, D., Lee, P.L. et al. Nucleic Acids Res (2021) 49:e52-e52. DOI 10.1093/nar/gkab070 · PubMed
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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