Bipartite interaction of TOPBP1 with the GINS complex
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8ok2
Q-score: 0.313
Day M, Tetik B, Parlak M, Almeida-Hernandez Y, Raschle M, Kaschani F, Siegert H, Marko A, Sanchez-Garcia E, Kaiser M, Barker IA, Pearl LH, Oliver AW, Boos D
Nat Commun (2024) 15 pp. 1797-1797 [ DOI: doi:10.1038/s41467-024-45946-0 Pubmed: 38413589 ]
- Dna replication complex gins protein sld5 (30 kDa, Protein from Homo sapiens)
- Topoisomerase (dna) ii binding protein 1 (52 kDa, Protein from Homo sapiens)
- Dna replication complex gins protein psf2 (21 kDa, Protein from Homo sapiens)
- Gins complex bound to topbp1 (Complex from Homo sapiens)
- Dna replication complex gins protein psf1 (17 kDa, Protein from Homo sapiens)
- Dna replication complex gins protein psf3 (24 kDa, Protein from Homo sapiens)
Resolution: 7.39 Å
EM Method: Single-particle
Fitted PDBs: 8w7s
Q-score: 0.212
Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y
Nat Commun (2023) 14 pp. 5849-5849 [ DOI: doi:10.1038/s41467-023-41506-0 Pubmed: 37730685 ]
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Replisome complex in state iv (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8kg6
Q-score: 0.437
Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y
Nat Commun (2023) 14 pp. 5849-5849 [ DOI: doi:10.1038/s41467-023-41506-0 Pubmed: 37730685 ]
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Replisome complex in state i (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae S288C)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 4.23 Å
EM Method: Single-particle
Fitted PDBs: 8kg8
Q-score: 0.246
Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y
Nat Commun (2023) 14 pp. 5849-5849 [ DOI: doi:10.1038/s41467-023-41506-0 Pubmed: 37730685 ]
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Replisome complex in state ii (1 MDa, Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae S288C)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 4.52 Å
EM Method: Single-particle
Fitted PDBs: 8kg9
Q-score: 0.19
Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y
Nat Commun (2023) 14 pp. 5849-5849 [ DOI: doi:10.1038/s41467-023-41506-0 Pubmed: 37730685 ]
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (70-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Replisome complex in state ii (1 MDa, Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 4.12 Å
EM Method: Single-particle
Fitted PDBs: 8w7m
Q-score: 0.267
Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y
Nat Commun (2023) 14 pp. 5849-5849 [ DOI: doi:10.1038/s41467-023-41506-0 Pubmed: 37730685 ]
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Replisome complex in state v (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
Structure of the S. cerevisiae replicative helicase CMG in complex with a forked DNA
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6u0m
Q-score: 0.219
Yuan Z, Georgescu R, Bai L, Zhang D, Li H, O'Donnell ME
Nat Commun (2020) 11 pp. 688- [ DOI: doi:10.1038/s41467-020-14577-6 ]
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (79 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (74 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (23 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (82 kDa, Protein from Saccharomyces cerevisiae)
- Dna (15-mer) (4 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Cell division control protein 45 (73 kDa, Protein from Saccharomyces cerevisiae)
- Dna (26-mer) (7 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (74 kDa, Protein from Saccharomyces cerevisiae)
- Cmg-forkdna (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (85 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (73 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae CMG-Pol epsilon-DNA
Resolution: 4.98 Å
EM Method: Single-particle
Fitted PDBs: 6hv9
Q-score: 0.231
Goswami P, Abid Ali F, Douglas ME, Locke J, Purkiss A, Janska A, Eickhoff P, Early A, Nans A, Cheung AMC, Diffley JFX, Costa A
Nat Commun (2018) 9 pp. 5061-5061 [ Pubmed: 30498216 DOI: doi:10.1038/s41467-018-07417-1 ]
- Dna polymerase epsilon catalytic subunit (104 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Cmg-pol epsilon (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*t)-3') (2 kDa, DNA from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Nucleic acid (Complex from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*ap*ap*ap*ap*cp*gp*gp*cp*cp*ap*gp*cp*gp*tp*gp*gp*cp*tp*gp*c)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(*gp*cp*ap*gp*cp*cp*ap*cp*gp*cp*tp*gp*gp*cp*cp*gp*tp*tp*tp*tp*a)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Cmg-pol epsilon-dna (Complex)