Structure of yeast replisome associated with FACT and histone hexamer, Composite map
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8xgc
Q-score: 0.407
Li N, Gao Y, Zhang Y, Yu D, Lin J, Feng J, Li J, Xu Z, Zhang Y, Dang S, Zhou K, Liu Y, Li XD, Tye BK, Li Q, Gao N, Zhai Y
Nature (2024) 627 pp. 890-897 [ DOI: doi:10.1038/s41586-024-07152-2 Pubmed: 38448592 ]
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b.2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna (51-mer) (15 kDa, DNA from Saccharomyces cerevisiae)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of replication checkpoint protein 1 (124 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Endogenous replisomes (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (29 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae)
- Fact complex subunit spt16 (118 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae)
- Fact complex subunit pob3 (63 kDa, Protein from Saccharomyces cerevisiae)
- Dna (39-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 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)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Topoisomerase 1-associated factor 1 (141 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 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 mcm2 (98 kDa, Protein from Saccharomyces cerevisiae S288C)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae S288C)
Cryo-EM structure of MCM double hexamer with structured Mcm4-NSD
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7v3u
Q-score: 0.514
Cheng J, Li N, Huo Y, Dang S, Tye BK, Gao N, Zhai Y
Nat Commun (2022) 13 pp. 1396-1396 [ DOI: doi:10.1038/s41467-022-29070-5 Pubmed: 35296675 ]
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Mcm double hexamer (dh) (Complex from Saccharomyces cerevisiae S288c)
- Dna replication licensing factor mcm7 (95 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 ]
- Minichromosome maintenance protein 5 (74 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (74 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (23 kDa, Protein from Saccharomyces cerevisiae)
- Dna (26-mer) (7 kDa, DNA from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna (15-mer) (4 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (82 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (85 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (79 kDa, Protein from Saccharomyces cerevisiae)
- Cmg-forkdna (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (73 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (73 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of Mcm2-7 double hexamer on dsDNA
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 5bk4
Q-score: 0.393
Noguchi Y, Yuan Z, Bai L, Schneider S, Zhao G, Stillman B, Speck C, Li H
PNAS (2017) 114 pp. E9529-E9538 [ DOI: doi:10.1073/pnas.1712537114 Pubmed: 29078375 ]
- Dna (60-mer), strand 2 (18 kDa, DNA from Saccharomyces cerevisiae)
- Mcm double hexamer (Complex from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication licensing factor mcm5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna (60-mer), strand 1 (18 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Mcm double hexamer bound to double-stranded dna (Complex from Saccharomyces cerevisiae)
- Synthetic double-stranded dna (Complex from Saccharomyces cerevisiae)
Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1
Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C, Chen ZA, Barbon M, Rappsilber J, Stillman B, Speck C, Li H
Nat Struct Mol Biol (2017) 24 pp. 316-324 [ Pubmed: 28191893 DOI: doi:10.1038/nsmb.3372 ]
- Origin recognition complex subunit 1 (104 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Origin recognition complex subunit 2 (71 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (39-mer) (12 kDa, DNA from synthetic construct)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Origin recognition complex subunit 3 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Cell division cycle protein cdt1 (68 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Cell division control protein 6 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Origin recognition complex subunit 6 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Origin recognition complex subunit 5 (55 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Origin recognition complex subunit 4 (60 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (39-mer) (11 kDa, DNA from synthetic construct)
- Orc-cdc6-cdt1-mcm2-7 (Complex from Saccharomyces cerevisiae)
Structure of Ctf4 trimer in complex with one CMG helicase
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6ptj
Q-score: 0.414
Yuan Z, Georgescu R, Santos RLA, Zhang D, Bai L, Yao NY, Zhao G, O'Donnell ME, Li H
eLife (2019) 8 [ Pubmed: 31589141 DOI: doi:10.7554/eLife.47405 ]
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Cmg-ctf4 (Complex from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication licensing factor mcm6 (113 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 (strain ATCC 204508 / S288c))