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Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8jnd
Q-score: 0.19
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)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 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)
- Rad51-nucleosome complex (Complex from Homo sapiens)
Resolution: 4.68 Å
EM Method: Single-particle
Fitted PDBs: 8jne
Q-score: 0.13
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)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 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)
- Rad51-nucleosome complex (Complex 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)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 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)
- Rad51-nucleosome complex (Complex from Homo sapiens)
Resolution: 4.12 Å
EM Method: Single-particle
Fitted PDBs: 8xbt
Q-score: 0.199
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)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 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)
- Rad51-nucleosome complex (Complex from Homo sapiens)
Resolution: 4.24 Å
EM Method: Single-particle
Fitted PDBs: 8xbu
Q-score: 0.171
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)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 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)
- Rad51-nucleosome complex (Complex from Homo sapiens)
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8xbw
Q-score: 0.219
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*ap*cp*gp*tp*gp*cp*gp*tp*tp*tp*ap*ap*gp*cp*gp*gp*t)-3') (47 kDa, DNA from synthetic construct)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*ap*cp*cp*gp*cp*tp*tp*ap*ap*ap*cp*gp*cp*ap*cp*gp*tp*a)-3') (47 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex from Homo sapiens)
Structure of nucleosome-bound SRCAP-C in the apo state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8x15
Q-score: 0.218
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
Cell Discov (2024) 10 pp. 15-15 [ DOI: doi:10.1038/s41421-023-00640-1 Pubmed: 38331872 ]
- Yeats domain-containing protein 4 (26 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (137-mer) (41 kDa, DNA from synthetic construct)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Helicase srcap (343 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Zinc finger hit domain-containing protein 1 (17 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Dna (137-mer) (42 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1, n-terminally processed (41 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin-related protein 6 (45 kDa, Protein from Homo sapiens)
- Structure of nucleosome-bound srcap-c in the apo state (Complex from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8x19
Q-score: 0.292
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
Cell Discov (2024) 10 pp. 15-15 [ DOI: doi:10.1038/s41421-023-00640-1 Pubmed: 38331872 ]
- Yeats domain-containing protein 4 (26 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Helicase srcap (343 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Zinc finger hit domain-containing protein 1 (17 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Structure of nucleosome-bound srcap-c in the adp-befx-bound state (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin-related protein 6 (45 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
Structure of nucleosome-bound SRCAP-C in the ADP-bound state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8x1c
Q-score: 0.297
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
Cell Discov (2024) 10 pp. 15-15 [ DOI: doi:10.1038/s41421-023-00640-1 Pubmed: 38331872 ]
- Yeats domain-containing protein 4 (26 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Helicase srcap (343 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Zinc finger hit domain-containing protein 1 (17 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
- Structure of nucleosome-bound srcap-c in the adp-bound state (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Actin, cytoplasmic 1 (41 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin-related protein 6 (45 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8rbx
Q-score: 0.037
Fianu I, Ochmann M, Walshe JL, Dybkov O, Cruz JN, Urlaub H, Cramer P
Nature (2024) 629 pp. 219-227 [ DOI: doi:10.1038/s41586-024-07269-4 Pubmed: 38570683 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna and dna (Complex from Sus scrofa)
- Integrator complex subunit 10 (82 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Template dna (56 kDa, DNA from synthetic construct)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (65 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Homo sapiens)
- Histone h3.3c (15 kDa, Protein from Homo sapiens)
- Rna (5 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Integrator complex subunit 14 (57 kDa, Protein from Homo sapiens)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Dsif (Complex from Trichoplusia ni)
- Nelf-b,negative elongation factor b,negative elongation factor b,negative elongation factor b,negative elongation factor b,negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Integrator-pp2a complex and nelf (Complex from Homo sapiens)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dss1 (3 kDa, Protein from Trichoplusia ni)
- Histone h2a type 1 (14 kDa, Protein from Homo sapiens)
- Integrator complex subunit 15 (50 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Integrator complex subunit 13 (80 kDa, Protein from Homo sapiens)
- Integrator complex subunit 7 (107 kDa, Protein from Homo sapiens)
- Non-template dna (45 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk-unk (1 kDa, Protein from Homo sapiens)
- Unk-unk-unk-unk-unk-unk-unk-unk (698 Da, Protein from Sus scrofa)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Pre-termination complex (1 MDa, Complex)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)