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 h2b (10 kDa, Protein from Drosophila melanogaster)
- Template dna (53 kDa, DNA from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- 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)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (9 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb12 (5 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb1 (166 kDa, Protein from Drosophila melanogaster)
- Rna (3 kDa, RNA 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 rpabc3 (16 kDa, Protein from Drosophila melanogaster)
- Native purified nucleosome elongation complex from drosophila melanogaster (750 kDa, Complex from Drosophila melanogaster)
- Histone h3 (11 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Non-template dna (50 kDa, DNA from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb2 (132 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb3 (30 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 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Ubiquitin (8 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)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 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 ]
- Ncprc1-rybp (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Histones (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Dna (187-mer) (Complex from synthetic construct)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h1.4 (Complex from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2a (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histone h4 (Complex 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)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ncprc1rybp delta-linker mutant bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- 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)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 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 ]
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ncprc1rybp bound to unmodified nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8v4y
Q-score: 0.53
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (reverse strand) (64 kDa, DNA from synthetic construct)
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (63 kDa, DNA from synthetic construct)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Snf2h (100 kDa, Complex from Homo sapiens)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
Cryo-EM structure of doubly-bound SNF2h-nucleosome complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8v6v
Q-score: 0.477
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (reverse strand) (64 kDa, DNA from synthetic construct)
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (63 kDa, DNA from synthetic construct)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Snf2h (100 kDa, Complex from Homo sapiens)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8v7l
Q-score: 0.456
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (63 kDa, DNA from synthetic construct)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Snf2h (100 kDa, Complex from Homo sapiens)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (122 kDa, Protein from Homo sapiens)
- Widom 601 dna (147-mer) plus 60 base pairs flanking dna (reverse strand) (64 kDa, DNA from synthetic construct)
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 [ DOI: doi:10.7554/eLife.46057 Pubmed: 31210637 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (156-mer) (48 kDa, DNA from Xenopus laevis)
- Dna (156-mer) (47 kDa, DNA from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b (11 kDa, Protein from Xenopus laevis)
- Histone h2b (10 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)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (54 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)