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 ]
- Mediator of replication checkpoint protein 1 (124 kDa, Protein from Saccharomyces cerevisiae)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae)
- Dna (51-mer) (15 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (29 kDa, Protein from Saccharomyces cerevisiae)
- Endogenous replisomes (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Fact complex subunit pob3 (63 kDa, Protein 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)
- Zinc ion (65 Da, Ligand)
- Histone h3 (15 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)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b.2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna (39-mer) (11 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 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 ]
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae S288C)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Replisome complex in state i (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- 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)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae S288C)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
S. cerevisiae pol alpha - replisome complex
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 8b9c
Q-score: 0.217
Jones ML, Aria V, Baris Y, Yeeles JTP
Mol Cell (2023) 83 pp. 2911- [ Pubmed: 37506699 DOI: doi:10.1016/j.molcel.2023.06.035 ]
- Dna replication licensing factor mcm3 (111 kDa, Protein from Saccharomyces cerevisiae)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna primase small subunit (51 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45 (75 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (24 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna polymerase alpha subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Mediator of replication checkpoint protein 1 (126 kDa, Protein from Saccharomyces cerevisiae)
- S. cerevisiae replisome - pol alpha primase complex (Complex from Saccharomyces cerevisiae)
- Dna primase large subunit (62 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase alpha catalytic subunit a (167 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Lagging strand (32 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Leading strand (26 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation I)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7pmk
Q-score: 0.434
Jenkyn-Bedford M, Jones ML, Baris Y, Labib KPM, Cannone G, Yeeles JTP, Deegan TD
Nature (2021) 600 pp. 743-747 [ DOI: doi:10.1038/s41586-021-04145-3 Pubmed: 34700328 ]
- Dna replication licensing factor mcm3 (111 kDa, Protein from Saccharomyces cerevisiae)
- Cell division control protein 45,cell division control protein 45 (75 kDa, Protein from Saccharomyces cerevisiae)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae)
- Dna helicase (86 kDa, Protein from Saccharomyces cerevisiae)
- Lagging strand template dna (35 kDa, DNA from Synthetic construct)
- Replisome (Complex from Saccharomyces cerevisiae)
- E3 ubiquitin ligase complex scf subunit (22 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (22 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex from DNA molecule)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Protein dia2 (85 kDa, Protein from Saccharomyces cerevisiae)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Budding yeast replisome on double-stranded dna engaged with scf(dia2) (conformation i) (Complex)
- Magnesium ion (24 Da, Ligand)
- Leading strand template dna (37 kDa, DNA from Synthetic construct)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase alpha-binding protein (108 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7pmn
Q-score: 0.405
Jenkyn-Bedford M, Jones ML, Baris Y, Labib KPM, Cannone G, Yeeles JTP, Deegan TD
Nature (2021) 600 pp. 743-747 [ DOI: doi:10.1038/s41586-021-04145-3 Pubmed: 34700328 ]
- Dna replication licensing factor mcm3 (111 kDa, Protein from Saccharomyces cerevisiae)
- Budding yeast replisome on double-stranded dna engaged with scf(dia2) (conformation ii) (Complex)
- Leading strand template dna (37 kDa, DNA from Synthetic construct)
- Cell division control protein 45,cell division control protein 45 (75 kDa, Protein from Saccharomyces cerevisiae)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Replisome (Complex from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (22 kDa, Protein from Saccharomyces cerevisiae)
- Lagging strand template dna (35 kDa, DNA from Saccharomyces cerevisiae)
- Dna (Complex from DNA molecule)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Protein dia2 (85 kDa, Protein from Saccharomyces cerevisiae)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase alpha-binding protein (108 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Suppressor of kinetochore protein 1 (22 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the CMG Fork Protection Complex at a replication fork - Conformation 1
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6skl
Q-score: 0.352
Baretic D, Jenkyn-Bedford M, Aria V, Cannone G, Skehel M, Yeeles JTP
Mol Cell (2020) 78 pp. 926-940.e13 [ DOI: doi:10.1016/j.molcel.2020.04.012 Pubmed: 32369734 ]
- Conformation 1 of cmg-csm3-tof1-mrc1-ctf4 with a fork dna (1 MDa, Complex)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna fork, lagging-strand template (18 kDa, DNA from synthetic construct)
- Dna fork, leading-strand template (26 kDa, DNA from synthetic construct)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase alpha-binding protein (104 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))
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Chromosome segregation in meiosis protein 3 (36 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Cmg-csm3-tof1-mrc1-ctf4 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Topoisomerase 1-associated factor 1 (141 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna replication complex gins protein psf3 (24 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))
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))