6JXD: Histone H3.1
Human nucleosome core particle with cohesive end DNA termini. Determined by X-ray diffraction at 2.25 Å resolution. Released 15 Jan 2020.
- Method
- X-ray diffraction
- Resolution
- 2.25 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 12,227
- Mol. weight
- 179.14 kDa
- Ligands
- MN
- Released
- 15 Jan 2020
Explore 6JXD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6JXD contains 39 α-helices and 20 β-strands across 8 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: 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 | 97-98 | 2 | 3 |
Chain C: 6 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 | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 113-115 | 3 | |
Chains D and H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-119 | 19 | |
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 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-130 | 10 | |
Chain F: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-22 | 3 | |
| α-helix | 25-28 | 4 | |
| 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 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 3 |
| α-helix | 113-115 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.1 | A | protein | 98 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B | protein | 82 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C | protein | 107 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 97 | Homo sapiens | P06899 (AlphaFold model) |
| Histone H3.1 | E | protein | 97 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | F | protein | 87 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | G | protein | 106 | Homo sapiens | P04908 (AlphaFold model) |
| DNA (147-mer) | I | DNA | 147 | Homo sapiens | |
| DNA (147-mer) | J | DNA | 147 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>6JXD_1 Histone H3.1 (chains A)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 2 (B), FASTA
>6JXD_2 Histone H4 (chains B)
VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT
VTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C), FASTA
>6JXD_3 Histone H2A type 1-B/E (chains C)
RKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAAR
DNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK
Sequence of entity 4 (D, H), FASTA
>6JXD_4 Histone H2B type 1-J (chains D, H)
RKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRST
ITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Sequence of entity 5 (E), FASTA
>6JXD_5 Histone H3.1 (chains E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 6 (F), FASTA
>6JXD_6 Histone H4 (chains F)
KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH
AKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 7 (G), FASTA
>6JXD_7 Histone H2A type 1-B/E (chains G)
KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARD
NKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK
Sequence of entity 8 (I), FASTA
>6JXD_8 DNA (147-MER) (chains I)
CATATATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAAC
GCACGTACGCGCTGTCTACCGCGTTTTAACCGCCACTAGAAGCGCTTACTAGTCTCCAGG
CACGTGTGAGACCGGCATATATGGTAC
Sequence of entity 9 (J), FASTA
>6JXD_9 DNA (147-MER) (chains J)
CATATATGCCGGTCTCACACGTGCCTGGAGACTAGTAAGCGCTTCTAGTGGCGGTTAAAA
CGCGGTAGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAG
CGGCCTCGGCACCGGGATATATGGTAC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MN | Manganese (II) ion | Mn | 17 |
Primary citation
PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome. Sharma, D., De Falco, L., Padavattan, S. et al. Nat Commun (2019) 10:5751-5751. DOI 10.1038/s41467-019-13641-0 · 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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