Resolution: 8.8 Å
EM Method: Single-particle
Fitted PDBs: 7vvz
Q-score: 0.108
Qu K, Chen K, Wang H, Li X, Chen Z
Nature (2022) 610 pp. 569-574 [ Pubmed: 36198799 DOI: doi:10.1038/s41586-022-05303-x ]
- Histone acetyltransferase esa1 (52 kDa, Protein from Saccharomyces cerevisiae S288C)
- Chromatin modification-related protein eaf1 (133 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein yng2 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nua4 bound to the nucleosome (Complex from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Carboxymethyl coenzyme *a (825 Da, Ligand)
- Actin (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (207-mer) (64 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae S288C)
- Epl1 arginine anchor (1 kDa, Protein from Saccharomyces cerevisiae)
- Dna (207-mer) (63 kDa, DNA from Saccharomyces cerevisiae)
- Actin-related protein 4 (54 kDa, Protein from Saccharomyces cerevisiae S288C)
- Chromatin modification-related protein eaf6 (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-complex protein 4 (55 kDa, Protein from Saccharomyces cerevisiae S288C)
The ClassC RSC-Nucleosome Complex
Resolution: 10.13 Å
EM Method: Single-particle
Fitted PDBs: 6kw5
Q-score: 0.062
Ye YP, Wu H, Chen KJ, Verma N, Cairns B, Gao N, Chen ZC
To Be Published
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rsc (Complex from Saccharomyces cerevisiae S288c)
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
SWI/SNF nucleosome complex with ADP-BeFx
Resolution: 8.96 Å
EM Method: Single-particle
Fitted PDBs: 6uxw
Q-score: 0.122
Han Y, Reyes AA, Malik S, He Y
Nature (2020) 579 pp. 452-455 [ DOI: doi:10.1038/s41586-020-2087-1 Pubmed: 32188938 ]
- Transcription regulatory protein snf12 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription regulatory protein snf2 (194 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf complex subunit swi3 (93 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (5 kDa, Protein from Saccharomyces cerevisiae S288C)
- 601 sequence bottom strand (56 kDa, DNA from synthetic construct)
- Phosphate ion (94 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Transcription regulatory protein snf6 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swi/snf chromatin-remodeling complex subunit snf5 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf global transcription activator complex subunit swp82 (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Water (18 Da, Ligand)
- 601 sequence top strand (61 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf nucleosome complex with adp-befx (Complex from Saccharomyces cerevisiae)
- Beryllium trifluoride ion (66 Da, Ligand)
- Swi/snf chromatin-remodeling complex subunit swi1 (148 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome
Resolution: 9.9 Å
EM Method: Single-particle
Fitted PDBs: 6a5o
Q-score: 0.083
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ DOI: doi:10.1126/science.aau9904 Pubmed: 30287617 ]
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase ii elongation complex stalled at shl(-6) of the nucleosome (Complex from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*up*gp*gp*gp*up*gp*gp*up*gp*gp*c)-3') (3 kDa, RNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome
Resolution: 8.7 Å
EM Method: Single-particle
Fitted PDBs: 6a5r
Q-score: 0.11
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ DOI: doi:10.1126/science.aau9904 Pubmed: 30287617 ]
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*up*cp*up*cp*gp*up*gp*cp*cp*up*g)-3') (3 kDa, RNA from synthetic construct)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex stalled at shl(-2) of the nucleosome (Complex from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome
Resolution: 10.0 Å
EM Method: Single-particle
Fitted PDBs: 6g0l
Q-score: 0.095
Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T
eLife (2018) 7 [ DOI: doi:10.7554/eLife.35720 Pubmed: 30079888 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- X. laevis nucleosome pn 601 dna with s.cerevisiae remodeller chd1 (Complex from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- X. laevis nucleosome pn 601 dna with s.cerevisiae remodeller chd1 (Complex from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- X. laevis nucleosome pn 601 dna with s.cerevisiae remodeller chd1 (600 kDa, Complex)
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- X. laevis nucleosome pn 601 dna with s.cerevisiae remodeller chd1 (Complex from Xenopus laevis)
- Dna (176-mer) (54 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)