Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 9mu9
Q-score: 0.202
Venette-Smith NL, Vishwakarma RK, Dollinger R, Schultz J, Venkatakrishnan V, Babitzke P, Anand G, Gilmour DS, Armache J-P, Murakami K
To Be Published
- Dna-directed rna polymerase ii subunit rpb2 (132 kDa, Protein from Drosophila melanogaster)
- Template dna (53 kDa, DNA from Drosophila melanogaster)
- Native purified nucleosome elongation complex from drosophila melanogaster (750 kDa, Complex from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb9 (13 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (9 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Drosophila melanogaster)
- Non-template dna (50 kDa, DNA from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb1 (166 kDa, Protein from Drosophila melanogaster)
- Histone h3 (11 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Rna (3 kDa, RNA from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb5 (24 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb12 (5 kDa, Protein from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
- Histone h2b (10 kDa, Protein from Drosophila melanogaster)
PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vnv
Q-score: 0.357
Cookis T, Lydecker A, Sauer P, Kasinath V, Nogales E
Nat Struct Mol Biol (2025) [ Pubmed: 39774834 DOI: doi:10.1038/s41594-024-01452-x ]
- Prc2_aj1-450 bound to h3k36me3 modified nucleosome with tail engaged (Complex from Homo sapiens)
- Isoform 2 of histone-lysine n-methyltransferase ezh2 (85 kDa, Protein from Homo sapiens)
- Protein jumonji (49 kDa, Protein from Homo sapiens)
- Zinc finger protein aebp2 (31 kDa, Protein from Homo sapiens)
- Eed (50 kDa, Protein from Homo sapiens)
- Dna (26-mer) (8 kDa, DNA from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Rbap48 (47 kDa, Protein from Homo sapiens)
- Dna (26-mer) (7 kDa, DNA from Homo sapiens)
- H3k36me3-modified histone h3 (2 kDa, Protein from Homo sapiens)
PRC2_AJ119-450 bound to H3K4me3
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vmi
Q-score: 0.48
Cookis T, Lydecker A, Sauer P, Kasinath V, Nogales E
Nat Struct Mol Biol (2025) [ Pubmed: 39774834 DOI: doi:10.1038/s41594-024-01452-x ]
- Zinc ion (65 Da, Ligand)
- Histone h3.1 (747 Da, Protein from Homo sapiens)
- Polycomb protein suz12 (83 kDa, Protein from Homo sapiens)
- Protein jumonji (138 kDa, Protein from Homo sapiens)
- Histone h3.1t (1 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Ezh2 (85 kDa, Protein from Homo sapiens)
- Isoform 3 of zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Prc2_aj119-450 bound to h3k4me3-modified nucleosome (350 kDa, Complex from Homo sapiens)
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 ]
- Zinc ion (65 Da, Ligand)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 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 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Histone h4 (Complex from Xenopus laevis)
- Histone h1.4 (Complex from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2a (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Dna (187-mer) (Complex from synthetic construct)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1-rybp (Complex from Homo sapiens)
- 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)
- Zinc ion (65 Da, Ligand)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
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 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Zinc ion (65 Da, Ligand)
- Ncprc1rybp delta-linker mutant bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- 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 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Zinc ion (65 Da, Ligand)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1rybp bound to unmodified nucleosome (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 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)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
SWR1-nucleosome complex in configuration 1
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qku
Q-score: 0.363
Girvan P, Jalal ASB, McCormack EA, Skehan MT, Knight CL, Wigley DB, Rueda DS
Nature (2024) 636 pp. 251-257 [ DOI: doi:10.1038/s41586-024-08152-y Pubmed: 39506114 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h2a.2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
SWR1-nucleosome complex in configuration 2
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 8qkv
Q-score: 0.185
Girvan P, Jalal ASB, McCormack EA, Skehan MT, Knight CL, Wigley DB, Rueda DS
Nature (2024) 636 pp. 251-257 [ DOI: doi:10.1038/s41586-024-08152-y Pubmed: 39506114 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h2a.2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (194-mer) (60 kDa, DNA from synthetic construct)
- Vacuolar protein sorting-associated protein 72 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (194-mer) (59 kDa, DNA from synthetic construct)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8qyv
Q-score: 0.324
Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB
Mol Cell (2024) 84 pp. 3871- [ Pubmed: 39226902 DOI: doi:10.1016/j.molcel.2024.08.015 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (118-mer) (36 kDa, DNA from synthetic construct)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (118-mer) (36 kDa, DNA from synthetic construct)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-hexasome complex (Complex from Saccharomyces cerevisiae S288C)
- Swr1-complex protein 5 (34 kDa, Protein from Saccharomyces cerevisiae S288C)