ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9dby
Q-score: 0.39
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Map with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Dna (153-mer) (Complex from synthetic construct)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Dna (156-mer) (Complex from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
Map with best defined RING1B/BMI1 of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Dna (187-mer) (Complex from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
Composite map of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Dna (153-mer) (Complex from synthetic construct)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Dna (156-mer) (Complex from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Overall map of ncprc1rybp bound to doubly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (Protein from Homo sapiens)
- Histone h2a (Complex from Xenopus laevis)
- Dna (187-mer) (DNA from synthetic construct)
- Histone h4 (Protein from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Protein from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Dna (187-mer) (Complex from synthetic construct)
- Histone h3.2 (Protein from Xenopus laevis)
- Histone h3.2 (Complex from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Ubiquitin (Protein from Homo sapiens)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
ncPRC1RYBP bound to symmetric H2AK119Ub dinucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Histone h4 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (Protein)
- Histone h2a (Protein from Xenopus laevis)
- Ubiquitin (Protein)
- Dna (309-mer) (DNA from synthetic construct)
- Polycomb complex protein bmi-1 (Protein)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Protein)
- Histone h3.2 (Protein from Xenopus laevis)
Map focused on RYBP/Ub of ncPRC1RYBP bound to symmetric H2AK119Ub dinucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Dna (Complex from synthetic construct)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Dna (309-mer) (Complex from synthetic construct)
- Ubiquitin (Complex from Homo sapiens)
Map focused on RING1B/BMI1 of ncPRC1RYBP bound to symmetric H2AK119Ub dinucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Dna (Complex from synthetic construct)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Dna (309-mer) (Complex from synthetic construct)
- Ubiquitin (Complex from Homo sapiens)
Overall map of ncPRC1RYBP bound to asymmetric H2AK119Ub dinucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Dna (Complex from synthetic construct)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Dna (314-mer) (Complex from synthetic construct)
- Ubiquitin (Complex from Homo sapiens)
Map focused on RYBP/Ub of ncPRC1RYBP bound to asymmetric H2AK119Ub dinucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Dna (Complex from synthetic construct)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Dna (314-mer) (Complex from synthetic construct)
- Ubiquitin (Complex from Homo sapiens)