6LA8: Histone H3.1
349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0. Determined by X-ray diffraction at 3.4 Å resolution. Released 7 Oct 2020.
- Method
- X-ray diffraction
- Resolution
- 3.4 Å
- Organisms
- Homo sapiens, other sequences
- Chains
- 19
- Atoms
- 27,058
- Mol. weight
- 457.42 kDa
- Ligands
- CA
- Released
- 7 Oct 2020
Explore 6LA8 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6LA8 contains 79 α-helices and 43 β-strands across 17 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, E and O: 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, 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 | 3 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-71 | 26 | |
| 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 | |
| α-helix | 117-118 | 2 | |
Chains D, H, N and R: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Chains F and P: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| 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 | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chains G and M: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-71 | 26 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 113-115 | 3 | |
Chain K: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| 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 L: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 12 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 11 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 13 |
2 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 | protein | 136 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F, L, P | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G, M, Q | protein | 130 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-J | D, H, N, R | protein | 126 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (349-mer) | I | DNA | 349 | other sequences | |
| DNA (349-mer) | J | DNA | 349 | other sequences | |
| Histone H1.0 | S | protein | 194 | Homo sapiens | P07305 |
Sequence of entity 1 (A, E, K, O), FASTA
>6LA8_1 Histone H3.1 (chains A, E, K, O)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F, L, P), FASTA
>6LA8_2 Histone H4 (chains B, F, L, P)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G, M, Q), FASTA
>6LA8_3 Histone H2A type 1-B/E (chains C, G, M, Q)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 4 (D, H, N, R), FASTA
>6LA8_4 Histone H2B type 1-J (chains D, H, N, R)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (I), FASTA
>6LA8_5 DNA (349-MER) (chains I)
CGCTGGAAAAAAAAAACGCATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCT
AGCACCGCTTAAACGCACGTACGCGCTGTCTACCGCGTTTTAACCGCCACTAGAAGCGCT
TACTAGTCTCCAGGCACGTGTGAGACCGGCACATGAAAAAAAAAAGCATGCTCGAGTATG
AAAAAAAAAACGCATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACC
GCTTAAACGCACGTACGCGCTGTCTACCGCGTTTTAACCGCCACTAGAAGCGCTTACTAG
TCTCCAGGCACGTGTGAGACCGGCACATGAAAAAAAAAACCAGCGGTAC
Sequence of entity 6 (J), FASTA
>6LA8_6 DNA (349-MER) (chains J)
CGCTGGTTTTTTTTTTCATGTGCCGGTCTCACACGTGCCTGGAGACTAGTAAGCGCTTCT
AGTGGCGGTTAAAACGCGGTAGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTC
TACGACCAATTGAGCGGCCTCGGCACCGGGATGCGTTTTTTTTTTCATACTCGAGCATGC
TTTTTTTTTTCATGTGCCGGTCTCACACGTGCCTGGAGACTAGTAAGCGCTTCTAGTGGC
GGTTAAAACGCGGTAGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGAC
CAATTGAGCGGCCTCGGCACCGGGATGCGTTTTTTTTTTCCAGCGGTAC
Sequence of entity 7 (S), FASTA
>6LA8_7 Histone H1.0 (chains S)
MTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSHYKV
GENADSQIKLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKVATP
KKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTVKAKPVKASKPKKAKPVK
PKAKSSAKRAGKKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 23 |
Water and common crystallization additives (K) are not listed.
Primary citation
Near-atomic resolution structures of interdigitated nucleosome fibres. Adhireksan, Z., Sharma, D., Lee, P.L. et al. Nat Commun (2020) 11:4747-4747. DOI 10.1038/s41467-020-18533-2 · 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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