Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex)
Resolution: 7.14 Å
EM Method: Single-particle
Fitted PDBs: 9j8n
Q-score: 0.164
Horikoshi N, Miyake R, Sogawa-Fujiwara C, Ogasawara M, Takizawa Y, Kurumizaka H
Nat Commun (2025) 16 pp. 1495-1495 [ DOI: doi:10.1038/s41467-025-56823-9 Pubmed: 39929866 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Lamin-a/c (17 kDa, Protein from Homo sapiens)
- Barrier-to-autointegration factor (10 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Low mobility complex containing baf, lamin a/c igf, and nucleosome (620 kDa, Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
The cryo-EM structure of the RAD51 filament bound to the nucleosome
Resolution: 6.91 Å
EM Method: Single-particle
Fitted PDBs: 8jnf
Q-score: 0.143
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
Resolution: 7.61 Å
EM Method: Single-particle
Fitted PDBs: 8xbv
Q-score: 0.066
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]
- Dna (5'-d(p*tp*gp*gp*cp*cp*gp*tp*tp*tp*tp*cp*g)-3') (47 kDa, DNA from synthetic construct)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*cp*gp*ap*ap*ap*ap*cp*gp*gp*cp*cp*ap*cp*cp*a)-3') (47 kDa, DNA from synthetic construct)
Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 8xby
Q-score: 0.061
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ Pubmed: 38509361 DOI: doi:10.1038/s41586-024-07196-4 ]
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*ap*ap*cp*gp*ap*ap*ap*ap*cp*gp*gp*cp*cp*ap*cp*cp*ap*cp*g)-3') (48 kDa, DNA from synthetic construct)
- Dna (5'-d(p*cp*gp*tp*gp*gp*tp*gp*gp*cp*cp*gp*tp*tp*tp*tp*cp*gp*tp*t)-3') (48 kDa, DNA from synthetic construct)
Resolution: 7.64 Å
EM Method: Single-particle
Fitted PDBs: 8ihl
Q-score: 0.109
Nishimura M, Fujii T, Tanaka H, Maehara K, Morishima K, Shimizu M, Kobayashi Y, Nozawa K, Takizawa Y, Sugiyama M, Ohkawa Y, Kurumizaka H
Commun Biol (2024) 7 pp. 61-61 [ DOI: doi:10.1038/s42003-023-05694-1 Pubmed: 38191828 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (353-mer) (108 kDa, DNA from synthetic construct)
- Overlapping tri-nucleosome (511 kDa, Complex from Homo sapiens)
- Dna (353-mer) (109 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Resolution: 7.1 Å
EM Method: Single-particle
Fitted PDBs: 7wbw
Q-score: 0.137
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol (2023) 435 pp. 168130-168130 [ Pubmed: 37120012 DOI: doi:10.1016/j.jmb.2023.168130 ]
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Histone (Complex)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-3.5) of the nucleosome (Complex from Komagataella phaffii)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna, rna (Complex)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*gp*up*up*up*up*cp*gp*up*up*gp*up*up*up*up*up*u)-3') (4 kDa, RNA from synthetic construct)
Resolution: 6.95 Å
EM Method: Single-particle
Fitted PDBs: 8he5
Q-score: 0.105
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol (2023) 435 pp. 168130-168130 [ Pubmed: 37120012 DOI: doi:10.1016/j.jmb.2023.168130 ]
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii elongation complex bound with rad26 and elf1, stalled at shl(-3.5) of the nucleosome (Complex from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Dna repair protein (125 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Dna, rna (Complex from Komagataella phaffii)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Rad26 (Complex from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Transcription elongation factor elf1 (Complex)
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Histone (Complex from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*gp*up*up*up*up*cp*gp*up*up*gp*up*up*up*up*up*u)-3') (4 kDa, RNA from synthetic construct)
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 ]
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 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)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor 1 homolog (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 abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 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 h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Rna polymerase subunit abc10-beta (8 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Spt5 (101 kDa, Protein 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))
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 [ DOI: doi:10.1126/science.aau9904 Pubmed: 30287617 ]
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 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 elongation complex stalled at shl(-5) of the nucleosome (Complex from Komagataella phaffii)
- Magnesium ion (24 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))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 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 h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*gp*gp*gp*up*gp*gp*up*gp*gp*c)-3') (3 kDa, RNA from synthetic construct)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 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 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 [ DOI: doi:10.1126/science.aau9904 Pubmed: 30287617 ]
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 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 elongation complex stalled at shl(-5) of the nucleosome (Complex from Komagataella phaffii)
- Magnesium ion (24 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))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 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))
- Rna (5'-r(p*gp*gp*up*gp*up*cp*up*up*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))