RAD51 nucleoprotein filament on abasic single-stranded DNA
Hanthi YW, Ramirez-Otero MA, Appleby R, De Antoni A, Joudeh L, Sannino V, Waked S, Ardizzoia A, Barra V, Fachinetti D, Pellegrini L, Costanzo V
Mol Cell (2024) 84 pp. 3026-3043.e11 [ Pubmed: 39178838 DOI: doi:10.1016/j.molcel.2024.07.004 ]
- Calcium ion (40 Da, Ligand)
- Dna (5'-d(p*gp*gp*(3dr)p*ap*tp*(3dr)p*cp*ap*(3dr)p*tp*gp*(3dr)p*tp*ap*(3dr)p*ap*cp*(3dr)p*tp*gp*(3dr)p*gp*c)-3') (6 kDa, DNA from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Rad51 nucleoprotein filament (Complex from Homo sapiens)
RAD51 nucleoprotein filament on double-stranded abasic DNA
Hanthi YW, Ramirez-Otero MA, Appleby R, De Antoni A, Joudeh L, Sannino V, Waked S, Ardizzoia A, Barra V, Fachinetti D, Pellegrini L, Costanzo V
Mol Cell (2024) 84 pp. 3026-3043.e11 [ Pubmed: 39178838 DOI: doi:10.1016/j.molcel.2024.07.004 ]
- Dna (5'-d(p*tp*gp*(3dr)p*tp*gp*(3dr)p*tp*gp*(3dr)p*tp*gp*(3dr)p*tp*gp*(3dr)p*tp*gp*(3dr)p*tp*gp*(3dr)p*tp*g)-3') (6 kDa, DNA from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Dna (5'-d(p*cp*ap*cp*cp*ap*cp*cp*ap*cp*cp*ap*cp*cp*ap*cp*cp*ap*cp*cp*ap*cp*cp*a)-3') (6 kDa, DNA from Homo sapiens)
- Rad51 nucleoprotein filament on double-stranded abasic dna (Complex)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna repair protein (Complex from Homo sapiens)
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 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein 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 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 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 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein 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 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein 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 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Rad51-nucleosome complex (Complex 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)
- Dna (5'-d(p*tp*gp*gp*cp*cp*gp*tp*tp*tp*tp*cp*g)-3') (47 kDa, DNA from synthetic construct)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
Resolution: 4.36 Å
EM Method: Single-particle
Fitted PDBs: 8xbx
Q-score: 0.072
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex 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 Escherichia coli)
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 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- 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)