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)
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a (Complex from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histones (Complex from Xenopus laevis)
- Dna (156-mer) (Complex from synthetic construct)
- Histone h3.2 (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Dna (153-mer) (Complex from synthetic construct)
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8jnd
Q-score: 0.19
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Resolution: 4.68 Å
EM Method: Single-particle
Fitted PDBs: 8jne
Q-score: 0.13
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
The cryo-EM structure of the RAD51 filament bound to the nucleosome
Resolution: 6.91 Å
EM Method: Single-particle
Fitted PDBs: 8jnf
Q-score: 0.143
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Resolution: 4.12 Å
EM Method: Single-particle
Fitted PDBs: 8xbt
Q-score: 0.199
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Resolution: 4.24 Å
EM Method: Single-particle
Fitted PDBs: 8xbu
Q-score: 0.171
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6ne3
Q-score: 0.42
Armache JP, Gamarra N, Johnson SL, Leonard JD, Wu S, Narlikar GJ, Cheng Y
eLife (2019) 8 [ Pubmed: 31210637 DOI: doi:10.7554/eLife.46057 ]
- Dna (156-mer) (48 kDa, DNA from Xenopus laevis)
- Histone h2b (11 kDa, Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (54 kDa, Protein from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Cryo-em structure of singly-bound snf2h-nucleosome complex with snf2h bound at the flanking dna proximal side (340 MDa, Complex from Xenopus laevis)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)