6M4H: Histone H3.1
Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2. Determined by electron microscopy at 3.9 Å resolution. Released 23 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 9,420
- Mol. weight
- 197.78 kDa
- Released
- 23 Sept 2020
Explore 6M4H in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6M4H contains 32 α-helices and 16 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.
Chains A and E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-74 | 11 | |
| α-helix | 75-77 | 3 | |
| 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 | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-91 | 9 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-24 | 4 | |
| α-helix | 31-39 | 9 | |
| β-strand | 46 | 1 | 4 |
| α-helix | 53-77 | 25 | |
| α-helix | 84-92 | 9 | |
| β-strand | 104-106 | 3 | 5 |
Chains D and H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| α-helix | 57-83 | 27 | |
| β-strand | 88 | 1 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-122 | 18 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 5 |
Chain G: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-24 | 4 | |
| α-helix | 31-39 | 9 | |
| β-strand | 46 | 1 | 8 |
| α-helix | 51-75 | 25 | |
| α-helix | 84-92 | 9 | |
| β-strand | 105-106 | 2 | 3 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| DNA (103-mer) | I | DNA | 147 | Homo sapiens | |
| DNA (103-mer) | J | DNA | 147 | Homo sapiens | |
| Histone H3.1 | A, E | protein | 136 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A-Bbd type 2/3 | C, G | protein | 115 | Homo sapiens | P0C5Z0 (AlphaFold model) |
| Histone H2B type 2-E | D, H | protein | 126 | Homo sapiens | Q16778 (AlphaFold model) |
Sequence of entity 1 (I), FASTA
>6M4H_1 DNA (103-MER) (chains I)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 2 (J), FASTA
>6M4H_2 DNA (103-MER) (chains J)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 3 (A, E), FASTA
>6M4H_3 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 4 (B, F), FASTA
>6M4H_4 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 5 (C, G), FASTA
>6M4H_5 Histone H2A-Bbd type 2/3 (chains C, G)
MPRRRRRRGSSGAGGRGRTCSRTVRAELSFSVSQVERSLREGHYAQRLSRTAPVYLAAVI
EYLTAKVLELAGNEAQNSGERNITPLLLDMVVHNDRLLSTLFNTTTISQVAPGED
Sequence of entity 6 (D, H), FASTA
>6M4H_6 Histone H2B type 2-E (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK
Primary citation
Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2. Zhou, M., Dai, L., Li, C. et al. EMBO J (2021) 40:e105907-e105907. DOI 10.15252/embj.2020105907 · 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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