8PP7: Human RYBP-PRC1
human RYBP-PRC1 bound to mononucleosome. Determined by electron microscopy at 2.91 Å resolution. Released 27 Mar 2024.
- Method
- Electron microscopy
- Resolution
- 2.91 Å
- Organisms
- Homo sapiens, Drosophila melanogaster
- Chains
- 14
- Atoms
- 15,562
- Mol. weight
- 413.74 kDa
- Ligands
- ZN
- Released
- 27 Mar 2024
Explore 8PP7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8PP7 contains 60 α-helices and 50 β-strands across 12 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 | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 15 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 16 |
| 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 | 46 | 1 | 16 |
| α-helix | 51-75 | 25 | |
| β-strand | 80-81 | 2 | 15 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-98 | 3 | 17 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-20 | 5 | |
| α-helix | 26-34 | 9 | |
| β-strand | 41-42 | 2 | 18 |
| α-helix | 46-71 | 26 | |
| α-helix | 79-88 | 10 | |
| α-helix | 90-95 | 6 | |
| β-strand | 99-101 | 3 | 19 |
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 | 18 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-119 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-42 | 3 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 20 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 21 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 21 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 20 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 19 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-20 | 5 | |
| α-helix | 26-35 | 10 | |
| β-strand | 41-42 | 2 | 22 |
| α-helix | 46-71 | 26 | |
| β-strand | 76-77 | 2 | 23 |
| α-helix | 79-87 | 9 | |
| α-helix | 90-95 | 6 | |
| β-strand | 99-101 | 3 | 17 |
| 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 | 23 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 22 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
4 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 |
|---|
| Polycomb complex protein BMI-1 | K, M | protein | 335 | Homo sapiens | P35226 (AlphaFold model) |
| E3 ubiquitin-protein ligase RING2 | L, N | protein | 340 | Homo sapiens | Q99496 (AlphaFold model) |
| 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 |
| Histone H2B | D, H | protein | 123 | Drosophila melanogaster | P02283 |
| DNA (215-mer) | J | DNA | 248 | Homo sapiens | |
| DNA (215-mer) | I | DNA | 248 | Homo sapiens | |
Sequence of entity 1 (K, M), FASTA
>8PP7_1 Polycomb complex protein BMI-1 (chains K, M)
MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQV
HKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADE
DKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLR
SKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMKISHQR
DGLTNAGELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSP
SGNHQSSFANRPRKSSVNGSSATSSGGMKHHHHHH
Sequence of entity 2 (L, N), FASTA
>8PP7_2 E3 ubiquitin-protein ligase RING2 (chains L, N)
GPDSMSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLD
MLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPS
RDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGDS
SHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASEIELVFRPHPTL
MEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIA
TASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK
Sequence of entity 3 (A, E), FASTA
>8PP7_3 Histone H3 (Fragment) (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 4 (B, F), FASTA
>8PP7_4 Histone H4 (chains B, F)
MITGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL
KVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 5 (C, G), FASTA
>8PP7_5 Histone H2A (chains C, G)
SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE
VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE
KKA
Sequence of entity 6 (D, H), FASTA
>8PP7_6 Histone H2B (chains D, H)
MPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIM
NSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SSK
Sequence of entity 7 (J), FASTA
>8PP7_7 DNA (215-mer) (chains J)
CCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGATATCCCGAGTCGCTGTTCAATAAATA
CACAGGATGTATATATCTGACACGTGCCTGGAGATTAGGGAGTAATCCCCTTGGCGGTTA
AAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATT
GAGCGGCCTCGGCACCGGGATTCTCCAGGTCCGCCGCGTATAGGGTCCATCACATAAGCC
CGAGATAT
Sequence of entity 8 (I), FASTA
>8PP7_8 DNA (215-mer) (chains I)
ATATCTCGGGCTTATGTGATGGACCCTATACGCGGCGGACCTGGAGAATCCCGGTGCCGA
GGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCC
CCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATAC
ATCCTGTGTATGTATTGAACAGCGACTCGGGATATCTCTAGAGTCGACCTGCAGGCATGC
AAGCTTGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 8 |
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 P35226 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6WI7 1.7 Å, RING1B-BMI1 fusion in closed conformation
- 2H0D 2.5 Å, Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex
- 5FR6 2.51 Å, The structure of polycomb ULD complex
- 3RPG 2.65 Å, Bmi1/Ring1b-UbcH5c complex structure
- 28OE 2.74 Å, Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
- 9DBY 2.8 Å, ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
- 9V9Q 2.8 Å, Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified…
- 9DGG 2.98 Å, ncPRC1RYBP bound to unmodified nucleosome
- 9V6S 3.0 Å, Cryo-EM structure of a single cPRC1 complex engaged on one face of an endogenous 147-bp…
- 8GRM 3.05 Å, Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome
- 6WI8 3.09 Å, Inhibitor compound-induced confrontational change in Ring1b-Bmi1 domain structure
- 9DDE 3.2 Å, ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Browse structure collections
About this viewer
MolViewer shows 8PP7 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.