Structure of a native Drosophila melanogaster octameric nucleosome
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 9mu4
Q-score: 0.442
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 (164-mer) (50 kDa, DNA from Drosophila melanogaster)
- Histone h3 (11 kDa, Protein from Drosophila melanogaster)
- Histone h2b (10 kDa, Protein from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
- Natively purified octameric nucleosome from drosophila melanogaster (240 MDa, Complex from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Dna (164-mer) (50 kDa, DNA from Drosophila melanogaster)
Structure of a native Drosophila melanogaster hexameric nucleosome
Resolution: 6.3 Å
EM Method: Single-particle
Fitted PDBs: 9mu5
Q-score: 0.206
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
- Histone h2b (10 kDa, Protein from Drosophila melanogaster)
- Histone h3 (10 kDa, Protein from Drosophila melanogaster)
- Natively purified hexameric nucleosome from drosophila melanogaster (220 MDa, Complex from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Dna (133-mer) (41 kDa, DNA from Drosophila melanogaster)
- Dna (133-mer) (40 kDa, DNA from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
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
- Histone h3 (11 kDa, Protein from Drosophila melanogaster)
- Histone h2b (10 kDa, Protein from Drosophila melanogaster)
- Native purified nucleosome elongation complex from drosophila melanogaster (750 kDa, Complex from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb2 (132 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb1 (166 kDa, Protein from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb12 (5 kDa, Protein 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 rpb9 (13 kDa, Protein from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
- Template dna (53 kDa, DNA from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb5 (24 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 polymerase ii subunit rpb3 (30 kDa, Protein from Drosophila melanogaster)
- Rna (3 kDa, RNA from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (9 kDa, Protein from Drosophila melanogaster)
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)
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a (Complex from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h4 (Complex from Xenopus laevis)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Dna (156-mer) (Complex from synthetic construct)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Dna (153-mer) (Complex from synthetic construct)
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a (Complex from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h4 (Complex from Xenopus laevis)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Dna (187-mer) (Complex from synthetic construct)
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)
- Histones (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h4 (Complex from Xenopus laevis)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Dna (156-mer) (Complex from synthetic construct)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Dna (153-mer) (Complex from synthetic construct)
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Ubiquitin (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h3.2 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histone h3.2 (Protein from Xenopus laevis)
- Overall map of ncprc1rybp bound to doubly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Protein from Homo sapiens)
- Dna (187-mer) (Complex from synthetic construct)
- Histone h4 (Protein from Xenopus laevis)
- Dna (187-mer) (DNA from synthetic construct)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (Protein from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Histone h2a (Protein from Xenopus laevis)
- Histones octamer (Complex from Xenopus laevis)
- Ubiquitin (Protein from Homo sapiens)
- Histone h2a (Complex from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Protein 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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2b 1.1 (Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Protein)
- Histone h4 (Protein from Xenopus laevis)
- Dna (309-mer) (DNA from synthetic construct)
- Ubiquitin (Protein)
- Histone h2a (Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (Protein)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h4 (Complex from Xenopus laevis)
- Histone h3.2 (Complex from Xenopus laevis)
- Dna (309-mer) (Complex from synthetic construct)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)