8JHF: Native SUV420H1
Native SUV420H1 bound to 167-bp nucleosome. Determined by electron microscopy at 3.68 Å resolution. Released 15 Nov 2023.
- Method
- Electron microscopy
- Resolution
- 3.68 Å
- Organism
- Homo sapiens
- Chains
- 11
- Atoms
- 14,703
- Mol. weight
- 236.83 kDa
- Ligands
- SAM, ZN
- Released
- 15 Nov 2023
Explore 8JHF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8JHF contains 45 α-helices and 30 β-strands across 9 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 6 |
| α-helix | 86-112 | 27 | |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 121-130 | 10 | |
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 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-93 | 11 | |
| β-strand | 98 | 1 | 8 |
Chain C: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-22 | 4 | |
| α-helix | 29-37 | 9 | |
| β-strand | 45-46 | 2 | 9 |
| α-helix | 50-70 | 21 | |
| α-helix | 74-76 | 3 | |
| α-helix | 83-92 | 10 | |
| α-helix | 94-99 | 6 | |
| β-strand | 104 | 1 | 10 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| α-helix | 54-80 | 27 | |
| β-strand | 85-86 | 2 | 9 |
| 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 | 45-54 | 10 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 11 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 12 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-21 | 2 | 4 |
| α-helix | 24-28 | 5 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 12 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 11 |
| α-helix | 83-93 | 11 | |
| β-strand | 98 | 1 | 10 |
Chain G: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-22 | 4 | |
| α-helix | 29-36 | 8 | |
| β-strand | 45-46 | 2 | 13 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 14 |
| α-helix | 83-92 | 10 | |
| α-helix | 94-99 | 6 | |
| β-strand | 104 | 1 | 8 |
| α-helix | 115-118 | 4 | |
| α-helix | 120-123 | 4 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 14 |
| α-helix | 54-80 | 27 | |
| β-strand | 85-86 | 2 | 13 |
| α-helix | 88-97 | 10 | |
| α-helix | 101-120 | 20 | |
1 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-lysine N-methyltransferase KMT5B | K | protein | 361 | Homo sapiens | Q4FZB7 (AlphaFold model) |
| Histone H3.1 | A, E | protein | 136 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 86 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A.Z | C, G | protein | 113 | Homo sapiens | P0C0S5 (AlphaFold model) |
| Histone H2B type 1-K | D, H | protein | 95 | Homo sapiens | O60814 |
| DNA (160-mer) | I | DNA | 160 | Homo sapiens | |
| DNA (160-mer) | J | DNA | 160 | Homo sapiens | |
Sequence of entity 1 (K), FASTA
>8JHF_1 Histone-lysine N-methyltransferase KMT5B (chains K)
MKWLGESKNMVVNGRRNGGKLSNDHQQNQSKLQHTGKDTLKAGKNAVERRSNRCNGNSGF
EGQSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFS
HNNPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKE
HVFIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEEN
MLLRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPG
EEISCYYGDGFFGENNEFCECYTCERRGTGAFKSRVGLPAPAPVINSKYGLRETDKRLNR
L
Sequence of entity 2 (A, E), FASTA
>8JHF_2 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 3 (B, F), FASTA
>8JHF_3 Histone H4 (chains B, F)
RHRMVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA
KRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 4 (C, G), FASTA
>8JHF_4 Histone H2A.Z (chains C, G)
KTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNA
SKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKGQQK
Sequence of entity 5 (D, H), FASTA
>8JHF_5 Histone H2B type 1-K (chains D, H)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Sequence of entity 6 (I), FASTA
>8JHF_6 DNA (160-MER) (chains I)
ATCCGATCCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAG
CACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCC
CTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTTCC
Sequence of entity 7 (J), FASTA
>8JHF_7 DNA (160-MER) (chains J)
GGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGT
TAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGAGCGGCCTCGGCACCGGGATTCTCCAGGGGATCGGAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SAM | S-adenosylmethionine | C15 H22 N6 O5 S | 1 |
| ZN | Zinc ion | Zn | 1 |
Primary citation
Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase. Lin, F., Zhang, R., Shao, W. et al. Cell Discov (2023) 9:120-120. DOI 10.1038/s41421-023-00620-5 · PubMed
Other PDB entries of the same protein (UniProt Q4FZB7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3S8P 1.85 Å, Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1…
- 8T68 1.9 Å, Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1…
- 5CPR 2.22 Å, The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity
- 5WBV 2.3 Å, Crystal Structure of the SET Domain of Human SUV420H1 In Complex With Inhibitor
- 8T9F 2.6 Å, Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
- 7YRD 3.2 Å, histone methyltransferase
- 8T9H 3.37 Å, Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
- 8JHG 3.58 Å, Native SUV420H1 bound to 167-bp nucleosome
- 7YRG 4.2 Å, histone methyltransferase
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