8PP6: Human RYBP-PRC1
human RYBP-PRC1 bound to H2AK118ub1 nucleosome. Determined by electron microscopy at 3.18 Å resolution. Released 3 Apr 2024.
- Method
- Electron microscopy
- Resolution
- 3.18 Å
- Organisms
- Drosophila melanogaster, Homo sapiens
- Chains
- 12
- Atoms
- 13,318
- Mol. weight
- 294.32 kDa
- Ligands
- ZN
- Released
- 3 Apr 2024
Explore 8PP6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8PP6 contains 45 α-helices and 30 β-strands across 10 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: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-39 | 3 | |
| α-helix | 41-42 | 2 | |
| α-helix | 46-56 | 11 | |
| 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 | 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 | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-20 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 41-42 | 2 | 4 |
| α-helix | 45-71 | 27 | |
| α-helix | 79-88 | 10 | |
| α-helix | 90-95 | 6 | |
| β-strand | 99-101 | 3 | 5 |
| α-helix | 112-114 | 3 | |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-39 | 3 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 84 | 1 | 6 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 81 | 1 | 6 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 5 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-20 | 5 | |
| α-helix | 26-34 | 9 | |
| β-strand | 41-42 | 2 | 8 |
| α-helix | 45-71 | 27 | |
| β-strand | 76-77 | 2 | 9 |
| α-helix | 79-88 | 10 | |
| α-helix | 90-95 | 6 | |
| β-strand | 99-101 | 3 | 3 |
| α-helix | 112-114 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 9 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 8 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-119 | 19 | |
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 (Fragment) | A, E | protein | 135 | Drosophila melanogaster | P02299 (AlphaFold model) |
| Histone H4 | B, F | protein | 104 | Drosophila melanogaster | P84040 (AlphaFold model) |
| Histone H2A | C, G | protein | 123 | Drosophila melanogaster | P84051 (AlphaFold model) |
| Histone H2B | D, H | protein | 123 | Drosophila melanogaster | P02283 (AlphaFold model) |
| DNA (215-mer) | I | DNA | 248 | Homo sapiens | |
| DNA (215-mer) | J | DNA | 248 | Homo sapiens | |
| RING1 and YY1-binding protein | K | protein | 232 | Homo sapiens | Q8N488 |
| Ubiquitin-40S ribosomal protein S27a (Fragment) | M | protein | 73 | Homo sapiens | P0CG47 |
Sequence of entity 1 (A, E), FASTA
>8PP6_1 Histone H3 (Fragment) (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8PP6_2 Histone H4 (chains B, F)
MITGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL
KVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8PP6_3 Histone H2A (chains C, G)
SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE
VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE
KKA
Sequence of entity 4 (D, H), FASTA
>8PP6_4 Histone H2B (chains D, H)
IPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIM
NSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SSK
Sequence of entity 5 (I), FASTA
>8PP6_5 DNA (215-MER) (chains I)
ATATCTCGGGCTTATGTGATGGACCCTATACGCGGCGGACCTGGAGAATCCCGGTGCCGA
GGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCC
CCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATAC
ATCCTGTGTATTTATTGAACAGCGACTCGGGATATCTCTAGAGTCGACCTGCAGGCATGC
AAGCTTGG
Sequence of entity 6 (J), FASTA
>8PP6_6 DNA (215-MER) (chains J)
CCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGATATCCCGAGTCGCTGTTCAATAAATA
CACAGGATGTATATATCTGACACGTGCCTGGAGATTAGGGAGTAATCCCCTTGGCGGTTA
AAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATT
GAGCGGCCTCGGCACCGGGATTCTCCAGGTCCGCCGCGTATAGGGTCCATCACATAAGCC
CGAGATAT
Sequence of entity 7 (K), FASTA
>8PP6_7 RING1 and YY1-binding protein (chains K)
GPDSMTMGDKKSPTRPKRQAKPAADEGFWDCSVCTFRNSAEAFKCSICDVRKGTSTRKPR
INSQLVAQQVAQQYATPPPPKKEKKEKVEKQDKEKPEKDKEISPSVTKKNTNKKTKPKSD
ILKDPPSEANSIQSANATTKTSETNHTSRPRLKNVDRSTAQQLAVTVGNVTVIITDFKEK
TRSSSTSSSTVTSSAGSEQQNQSSSGSESTDKGSSRSSTPKGDMSAVNDESF
Sequence of entity 8 (M), FASTA
>8PP6_8 Ubiquitin-40S ribosomal protein S27a (Fragment) (chains M)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1. Ciapponi, M., Karlukova, E., Schkolziger, S. et al. Nat Struct Mol Biol (2024) 31:1023-1027. DOI 10.1038/s41594-024-01258-x · PubMed
Other PDB entries of the same protein (UniProt P02299 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6AT0 1.28 Å, Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone…
- 6MHA 1.5 Å, dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine
- 6ASZ 1.52 Å, Chromodomain HP1 with Y24F mutation bound to histone H3 peptide containing trimethyl…
- 7VRF 1.7 Å, Crystal structure of Oxpecker chromodomain in complex with H3K9me3
- 1KNA 2.1 Å, Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
- 9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
- 2NQB 2.3 Å, Drosophila Nucleosome Structure
- 9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
- 1KNE 2.4 Å, Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9
- 2PYO 2.43 Å, Drosophila nucleosome core
- 8UX1 2.5 Å, Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
- 4QUF 2.5 Å, crystal structure of chromodomain of Rhino with H3K9me3
Browse structure collections
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