7D20: SET8-CENP-A-nucleosome complex
Cryo-EM structure of SET8-CENP-A-nucleosome complex. Determined by electron microscopy at 3.0 Å resolution. Released 10 Feb 2021.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 11
- Atoms
- 12,836
- Mol. weight
- 242.1 kDa
- Released
- 10 Feb 2021
Explore 7D20 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7D20 contains 38 α-helices and 31 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: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 48-55 | 8 | |
| α-helix | 64-74 | 11 | |
| α-helix | 88-113 | 26 | |
| β-strand | 120-121 | 2 | 1 |
| α-helix | 123-126 | 4 | |
| α-helix | 128-131 | 4 | |
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 | 3 |
| α-helix | 50-76 | 27 | |
| β-strand | 80-81 | 2 | 2 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 4 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 5 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 6 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 7 |
Chains D and H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 6 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 5 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-54 | 8 | |
| α-helix | 64-77 | 14 | |
| β-strand | 85-86 | 2 | 2 |
| α-helix | 88-109 | 22 | |
| β-strand | 120-121 | 2 | 3 |
| α-helix | 123-133 | 11 | |
Chain F: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 7 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 8 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 9 |
| α-helix | 80-89 | 10 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 4 |
Chain K: 4 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 195-212 | 18 | |
| β-strand | 218-223 | 6 | 10 |
| β-strand | 227-232 | 6 | 10 |
| β-strand | 236 | 1 | 11 |
| β-strand | 241-244 | 4 | 12 |
| β-strand | 248-250 | 3 | 13 |
| α-helix | 255-263 | 9 | |
| β-strand | 273-277 | 5 | 13 |
| β-strand | 280-285 | 6 | 13 |
| β-strand | 299 | 1 | 14 |
| β-strand | 306-312 | 7 | 12 |
| β-strand | 315-321 | 7 | 12 |
| β-strand | 326 | 1 | 11 |
| β-strand | 330-331 | 2 | 10 |
| α-helix | 332 | 1 | |
| β-strand | 334 | 1 | 14 |
| α-helix | 341-346 | 6 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3-like centromeric protein A | A, E | protein | 143 | Homo sapiens | P49450 (AlphaFold model) |
| Histone H4 | B, F | protein | 106 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G | protein | 133 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 129 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (145-mer) | I | DNA | 145 | synthetic construct | |
| DNA (145-mer) | J | DNA | 145 | synthetic construct | |
| Isoform 2 of N-lysine methyltransferase KMT5A | K | protein | 352 | Homo sapiens | Q9NQR1 |
Sequence of entity 1 (A, E), FASTA
>7D20_1 Histone H3-like centromeric protein A (chains A, E)
GSHMGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKS
THLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAG
RVTLFPKDVQLARRIRGLEEGLG
Sequence of entity 2 (B, F), FASTA
>7D20_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7D20_3 Histone H2A type 1-B/E (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>7D20_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSAK
Sequence of entity 5 (I), FASTA
>7D20_5 DNA (145-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT
Sequence of entity 6 (J), FASTA
>7D20_6 DNA (145-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT
Sequence of entity 7 (K), FASTA
>7D20_7 Isoform 2 of N-lysine methyltransferase KMT5A (chains K)
MARGRKMSKPRAVEAAAAAAAVAATAPGPEMVERRGPGRPRTDGENVFTGQSKIYSYMSP
NKCSGMRFPLQEENSVTHHEVKCQGKPLAGIYRKREEKRNAGNAVRSAMKSEEQKIKDAR
KGPLVPFPNQKSEAAEPPKTPPSSCDSTNAAIAKQALKKPIKGKQAPRKKAQGKTQQNRK
LTDFYPVRRSSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGD
FVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHS
KCGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH
Primary citation
Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase. Ho, C.H., Takizawa, Y., Kobayashi, W. et al. Life Sci Alliance (2021) 4. DOI 10.26508/lsa.202000919 · PubMed
Other PDB entries of the same protein (UniProt P49450 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5CVD 1.3 Å, Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide
- 6KDQ 1.5 Å, Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A…
- 6KDS 1.84 Å, Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A…
- 3NQJ 2.1 Å, Crystal structure of (CENP-A/H4)2 heterotetramer
- 7R5R 2.44 Å, Structure of the human CCAN CENP-A alpha-satellite complex
- 3NQU 2.5 Å, Crystal structure of partially trypsinized (CENP-A/H4)2 heterotetramer
- 5ZBX 2.58 Å, The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D)
- 3R45 2.6 Å, Structure of a CENP-A-Histone H4 Heterodimer in complex with chaperone HJURP
- 6E0P 2.6 Å, Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex…
- 6E0C 2.63 Å, Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain…
- 3WTP 2.67 Å, Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3
- 7PII 2.68 Å, Structure of the human CCAN CENP-A alpha-satellite complex
Browse structure collections
About this viewer
MolViewer shows 7D20 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.