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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9dde
Q-score: 0.456
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histones (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Histone h1.4 (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (Complex from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 9dg3
Q-score: 0.382
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ncprc1rybp delta-linker mutant bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
ncPRC1RYBP bound to unmodified nucleosome
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 9dgg
Q-score: 0.47
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ncprc1rybp bound to unmodified nucleosome (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8svf
Q-score: 0.383
Thomas JF, Valencia-Sanchez MI, Tamburri S, Gloor SL, Rustichelli S, Godinez-Lopez V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ
Sci Adv (2023) 9 pp. eadg9832-eadg9832 [ Pubmed: 37556531 DOI: doi:10.1126/sciadv.adg9832 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna/rna (327-mer) (102 kDa, Macromolecule from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Bap1/asxl1 bound to the h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase bap1 (80 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Polycomb group protein asxl1 (165 kDa, Protein from Homo sapiens)
- Dna/rna (187-mer) (58 kDa, Macromolecule from synthetic construct)