8PP6 image
Deposition Date 2023-07-06
Release Date 2024-04-03
Last Version Date 2025-07-09
Entry Detail
PDB ID:
8PP6
Keywords:
GENE REGULATION
Title:
human RYBP-PRC1 bound to H2AK118ub1 nucleosome
Biological Source:
Source Organism:
Drosophila melanogaster (Taxon ID: 7227)
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.18 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8PP6 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3 (Fragment)
Chain IDs:A, E
Chain Length:135
Number of Molecules:2
Biological Source:Drosophila melanogaster
UniProt ID:P02299 Pfam ID:PF00125
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:B, F
Chain Length:104
Number of Molecules:2
Biological Source:Drosophila melanogaster
UniProt ID:P84040 Pfam ID:PF15511
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A
Gene (Uniprot):His2A, His2A:CG31618, His2A:CG33808, His2A:CG33814, His2A:CG33817, His2A:CG33820, His2A:CG33823, His2A:CG33826, His2A:CG33829, His2A:CG33832, His2A:CG33835, His2A:CG33838, His2A:CG33841, His2A:CG33844, His2A:CG33847, His2A:CG33850, His2A:CG33862, His2A:CG33865
Chain IDs:C, G
Chain Length:123
Number of Molecules:2
Biological Source:Drosophila melanogaster
UniProt ID:P84051 Pfam ID:PF00125, PF16211
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B
Gene (Uniprot):His2B, His2B:CG17949, His2B:CG33868, His2B:CG33870, His2B:CG33872, His2B:CG33874, His2B:CG33876, His2B:CG33878, His2B:CG33880, His2B:CG33882, His2B:CG33884, His2B:CG33886, His2B:CG33888, His2B:CG33890, His2B:CG33892, His2B:CG33894, His2B:CG33896, His2B:CG33898, His2B:CG33900, His2B:CG33902, His2B:CG33904, His2B:CG33906, His2B:CG33908, His2B:CG33910
Chain IDs:D, H
Chain Length:123
Number of Molecules:2
Biological Source:Drosophila melanogaster
UniProt ID:P02283 Pfam ID:PF00125
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (215-MER)
Chain IDs:I
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (215-MER)
Chain IDs:J
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RING1 and YY1-binding protein
Gene (Uniprot):RYBP
Chain IDs:K
Chain Length:232
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N488 Pfam ID:PF00641, PF17219
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S27a (Fragment)
Chain IDs:L (auth: M)
Chain Length:73
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P0CG47 Pfam ID:PF00240
Ligand Molecules
ZN
Primary Citation
Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1.
Nat.Struct.Mol.Biol. 31 1023 1027 (2024)
PMID: 38528151 DOI: 10.1038/s41594-024-01258-x

Abstact

Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified nucleosomes via RING1B but H2Aub1-modified nucleosomes via RYBP. RYBP interactions with both ubiquitin and the nucleosome acidic patch create the high binding affinity that favors RYBP- over RING1B-directed PRC1 binding to H2Aub1-modified nucleosomes; this enables RING1B to monoubiquitinate H2A in neighboring unmodified nucleosomes.

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Disease

Primary Citation of related structures
8PP6