Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex
Resolution: 6.1 Å
EM Method: Single-particle
Fitted PDBs: 7y5v
Q-score: 0.222
Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM
Science (2023) 381 pp. eadd8673-eadd8673 [ Pubmed: 37616371 DOI: doi:10.1126/science.add8673 ]
- Chromatin assembly factor 1 subunit b (46 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- H3-h4 (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Chromatin assembly factor 1 subunit a (47 kDa, Protein from Homo sapiens)
- Caf1lc/rbbp4 (Complex from Homo sapiens)
- Dimeric caf1lc-h3-h4 complex (336 kDa, Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 8j6t
Q-score: 0.166
Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM
Science (2023) 381 pp. eadd8673-eadd8673 [ Pubmed: 37616371 DOI: doi:10.1126/science.add8673 ]
- Histone h4/h3.1 (Complex)
- Dna (Complex from Homo sapiens)
- Chromatin assembly factor 1 subunit a/b (Complex)
- Chromatin assembly factor 1 subunit a (107 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Chromatin assembly factor 1 subunit b (61 kDa, Protein from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- A double caf-1 bound right-handed di-tetrasome (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
Class1 of the INO80-Hexasome complex
Resolution: 6.68 Å
EM Method: Single-particle
Fitted PDBs: 8ett
Q-score: 0.186
Wu H, Munoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y
Science (2023) 381 pp. 319-324 [ DOI: doi:10.1126/science.adf4197 Pubmed: 37384669 ]
- Class1 hexasome in ino80-hexasome complex (Complex from Xenopus laevis)
- Dna (110-mer) (69 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (110-mer) (70 kDa, DNA from synthetic construct)
- 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)
The ClassA RSC-Nucleosome Complex
Resolution: 7.13 Å
EM Method: Single-particle
Fitted PDBs: 6kw3
Q-score: 0.086
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z
Science (2019) 366 pp. 838-843 [ Pubmed: 31672915 DOI: doi:10.1126/science.aay0033 ]
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc2 (102 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))
- Nuclear protein sth1/nps1 (156 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))
- Dna 167 (51 kDa, DNA from Homo sapiens)
- 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))
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc8 (63 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))
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
The ClassB RSC-Nucleosome Complex
Resolution: 7.55 Å
EM Method: Single-particle
Fitted PDBs: 6kw4
Q-score: 0.099
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z
Science (2019) 366 pp. 838-843 [ Pubmed: 31672915 DOI: doi:10.1126/science.aay0033 ]
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna 167 (51 kDa, DNA from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Chromatin structure-remodeling complex protein rsc30 (101 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))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Regulator of ty1 transposition protein 102 (17 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))
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rsc (Complex from Saccharomyces cerevisiae S288c)
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- High temperature lethal protein 1 (9 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))
Resolution: 7.9 Å
EM Method: Single-particle
Fitted PDBs: 6j4w
Q-score: 0.123
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI
Science (2019) 363 pp. 744-747 [ Pubmed: 30733384 DOI: doi:10.1126/science.aav8912 ]
- Rna polymerase subunit abc10-beta (8 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Spt5 (101 kDa, Protein from Komagataella pastoris)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-5) of the nucleosome (Complex from Komagataella pastoris)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*gp*up*gp*up*up*up*gp*gp*gp*up*gp*gp*up*gp*gp*c)-3') (5 kDa, RNA from synthetic construct)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- 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 polymerases i, ii, and iii subunit rpabc3 (16 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))
RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome
Resolution: 7.0 Å
EM Method: Single-particle
Fitted PDBs: 6a5p
Q-score: 0.138
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ Pubmed: 30287617 DOI: doi:10.1126/science.aau9904 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex stalled at shl(-5) of the nucleosome (Complex from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 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 (5'-r(p*up*gp*gp*gp*up*gp*gp*up*gp*gp*c)-3') (3 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- 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 polymerases i, ii, and iii subunit rpabc3 (16 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))
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome
Resolution: 6.7 Å
EM Method: Single-particle
Fitted PDBs: 6a5t
Q-score: 0.151
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ Pubmed: 30287617 DOI: doi:10.1126/science.aau9904 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex stalled at shl(-5) of the nucleosome (Complex from Komagataella phaffii)
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 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))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- 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 polymerases i, ii, and iii subunit rpabc3 (16 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))
Resolution: 7.6 Å
EM Method: Single-particle
Fitted PDBs: 6a5u
Q-score: 0.14
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ Pubmed: 30287617 DOI: doi:10.1126/science.aau9904 ]
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- 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 (40-mer) (12 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (198-mer) (61 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))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna, tilt conformation (Complex from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a, histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 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))
- Histone h2b, histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 6inq
Q-score: 0.149
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H
Science (2018) 362 pp. 595-598 [ Pubmed: 30287617 DOI: doi:10.1126/science.aau9904 ]
- Rna polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna (+1 position) (Complex from Komagataella phaffii)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Yeast)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Yeast)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Yeast)
- Rna polymerase ii subunit (18 kDa, Protein from Yeast)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Yeast)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Yeast)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Yeast)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna (5'-r(p*gp*up*gp*up*cp*up*up*gp*gp*gp*u)-3') (3 kDa, RNA from synthetic construct)
- Dna (198-mer) (38 kDa, DNA from synthetic construct)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Yeast)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Yeast)
- Histone h2a, histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Yeast)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Histone h2b, histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Yeast)