6LA9: Histone H3.1
349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant). Determined by X-ray diffraction at 3.7 Å resolution. Released 7 Oct 2020.
- Method
- X-ray diffraction
- Resolution
- 3.7 Å
- Organisms
- Homo sapiens, other sequences
- Chains
- 20
- Atoms
- 27,560
- Mol. weight
- 478.83 kDa
- Ligands
- CA
- Released
- 7 Oct 2020
Explore 6LA9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6LA9 contains 83 α-helices and 46 β-strands across 18 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, K 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 | |
Chains B, F and 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 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 3 |
Chains C 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 | 4 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 6 |
| α-helix | 113-115 | 3 | |
Chains D, H and N: 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 | |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 3 |
| α-helix | 113-115 | 3 | |
Chain M: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 14 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 15 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 16 |
| α-helix | 113-115 | 3 | |
Chain P: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 18 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 17 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 16 |
Chain R: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 20 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 19 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-124 | 21 | |
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, T | protein | 194 | Homo sapiens | P07305 |
Sequence of entity 1 (A, E, K, O), FASTA
>6LA9_1 Histone H3.1 (chains A, E, K, O)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F, L, P), FASTA
>6LA9_2 Histone H4 (chains B, F, L, P)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G, M, Q), FASTA
>6LA9_3 Histone H2A type 1-B/E (chains C, G, M, Q)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 4 (D, H, N, R), FASTA
>6LA9_4 Histone H2B type 1-J (chains D, H, N, R)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (I), FASTA
>6LA9_5 DNA (349-MER) (chains I)
CGCTGGAAAAAAAAAACGCATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCT
AGCACCGCTTAAACGCACGTACGCGCTGTCTACCGCGTTTTAACCGCCACTAGAAGCGCT
TACTAGTCTCCAGGCACGTGTGAGACCGGCACATGAAAAAAAAAAGCATGCTCGAGTATG
AAAAAAAAAACGCATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACC
GCTTAAACGCACGTACGCGCTGTCTACCGCGTTTTAACCGCCACTAGAAGCGCTTACTAG
TCTCCAGGCACGTGTGAGACCGGCACATGAAAAAAAAAACCAGCGGTAC
Sequence of entity 6 (J), FASTA
>6LA9_6 DNA (349-MER) (chains J)
CGCTGGTTTTTTTTTTCATGTGCCGGTCTCACACGTGCCTGGAGACTAGTAAGCGCTTCT
AGTGGCGGTTAAAACGCGGTAGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTC
TACGACCAATTGAGCGGCCTCGGCACCGGGATGCGTTTTTTTTTTCATACTCGAGCATGC
TTTTTTTTTTCATGTGCCGGTCTCACACGTGCCTGGAGACTAGTAAGCGCTTCTAGTGGC
GGTTAAAACGCGGTAGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGAC
CAATTGAGCGGCCTCGGCACCGGGATGCGTTTTTTTTTTCCAGCGGTAC
Sequence of entity 7 (S, T), FASTA
>6LA9_7 Histone H1.0 (chains S, T)
MTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSHYKV
GENADSQIKLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKVATP
KKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTVKAKPVKASKPKKAKPVK
PKAKSSAKRAGKKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 40 |
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
About this viewer
MolViewer shows 6LA9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.