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 ]
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
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 ]
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h4 (Complex from Xenopus laevis)
- Histone h3.2 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h1.4 (Complex from Homo sapiens)
- Histones (Complex from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1-rybp (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (Complex from synthetic construct)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Histone h2a (Complex from Xenopus laevis)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
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 ]
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h4 (11 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)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ncprc1rybp delta-linker mutant bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
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 h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Ncprc1rybp bound to unmodified nucleosome (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome
Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C
Sci Adv (2024) 10 pp. eadp0975-eadp0975 [ Pubmed: 39196936 DOI: doi:10.1126/sciadv.adp0975 ]
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dnmt3a1 udr in complex with h2ak119ub-nucleosome (Complex from Xenopus laevis)
- Dna (cytosine-5)-methyltransferase 3a (9 kDa, Protein from Homo sapiens)
- Dna (146-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Dna (146-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
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 h3.2 (15 kDa, Protein from Xenopus laevis)
- Polycomb group protein asxl1 (165 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase bap1 (80 kDa, Protein from Homo sapiens)
- Dna/rna (327-mer) (102 kDa, Macromolecule from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna/rna (187-mer) (58 kDa, Macromolecule from synthetic construct)
- Bap1/asxl1 bound to the h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Structure of the Marseillevirus nucleosome
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7lv8
Q-score: 0.431
Valencia-Sanchez MI, Abini-Agbomson S, Wang M, Lee R, Vasilyev N, Zhang J, De Ioannes P, La Scola B, Talbert P, Henikoff S, Nudler E, Erives A, Armache KJ
Nat Struct Mol Biol (2021) 28 pp. 413-417 [ DOI: doi:10.1038/s41594-021-00585-7 Pubmed: 33927388 ]
- Histone doublet delta-gamma (gamma) (11 kDa, Protein from Marseillevirus marseillevirus)
- Dna (123-mer) (37 kDa, DNA from synthetic construct)
- Histone doublet delta-gamma (delta) (10 kDa, Protein from Marseillevirus marseillevirus)
- Histone doublet beta-alpha (beta) (11 kDa, Protein from Marseillevirus marseillevirus)
- Structure of the marseillevirus nucleosome (Complex from synthetic construct)
- Dna (123-mer) (37 kDa, DNA from synthetic construct)
- Histone doublet beta-alpha (alpha) (17 kDa, Protein from Marseillevirus marseillevirus)
Marseillevirus heterotrimeric (hexameric) nucleosome
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7lv9
Q-score: 0.217
Valencia-Sanchez MI, Abini-Agbomson S, Wang M, Lee R, Vasilyev N, Zhang J, De Ioannes P, La Scola B, Talbert P, Henikoff S, Nudler E, Erives A, Armache KJ
Nat Struct Mol Biol (2021) 28 pp. 413-417 [ DOI: doi:10.1038/s41594-021-00585-7 Pubmed: 33927388 ]
- Histone doublet delta-gamma (gamma) (11 kDa, Protein from Marseillevirus marseillevirus)
- Dna (96-mer) (29 kDa, DNA from synthetic construct)
- Marseillevirus heterotrimeric (hexameric) nucleosome (Complex from synthetic construct)
- Histone doublet delta-gamma (delta) (10 kDa, Protein from Marseillevirus marseillevirus)
- Histone doublet beta-alpha (beta) (11 kDa, Protein from Marseillevirus marseillevirus)
- Dna (96-mer) (29 kDa, DNA from synthetic construct)
- Histone doublet beta-alpha (alpha) (17 kDa, Protein from Marseillevirus marseillevirus)
Active state Dot1 bound to the unacetylated H4 nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7k6p
Q-score: 0.473
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ DOI: doi:10.1126/science.abc6663 Pubmed: 33479126 ]
- Active state dot1 bound to the unacetylated h4 nucleosome (Complex from Saccharomyces cerevisiae)
- Polyubiquitin-b (Complex from Homo sapiens)
- Dna (146-mer) (Complex from synthetic construct)
- Dna (146-mer) (44 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Histones (Complex from Xenopus laevis)
- Histone h3.2 (11 kDa, Protein from Xenopus laevis)
- Histone h4 (10 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (46 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- S-adenosylmethionine (398 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
Active state Dot1 bound to the H4K16ac nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7k6q
Q-score: 0.489
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ DOI: doi:10.1126/science.abc6663 Pubmed: 33479126 ]
- Polyubiquitin-b (Complex from Homo sapiens)
- Dna (146-mer) (44 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Histones (Complex from Xenopus laevis)
- Histone h3.2 (11 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (Complex from Synthetic construct)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (46 kDa, Protein from Saccharomyces cerevisiae)
- Active state dot1 bound to the h4k16ac nucleosome (Complex from Saccharomyces cerevisiae)
- Histone h2a type 1 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- Histone h4 (10 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- S-adenosylmethionine (398 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)