S. cerevisiae nexus-sCMGE after DNA replication initiation
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8p5e
Q-score: 0.39
Henrikus SS, Gross MH, Willhoft O, Puhringer T, Lewis JS, McClure AW, Greiwe JF, Palm G, Nans A, Diffley JFX, Costa A
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01280-z Pubmed: 38760633 ]
- Dna (19-mer) (5 kDa, DNA from synthetic construct)
- Dna polymerase epsilon contains catalytic subunit a and non-catalytic subunit b (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (111 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 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 psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (25 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna (Complex from synthetic construct)
- Dna replication licensing factors mcm2-7 (Complex from Saccharomyces cerevisiae)
- Dna (7-mer) (2 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna replication complex gins containing psf1, psf2, psf3 and sld5 (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Cdc45 (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Complex of mcm2-7, cdc45, gins (psf1-3, sld5) dna polymerase epsilon (subunit a and b), 19-mer dna molecule with complementary 7-mer dna molecule (Complex 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)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae ssDNA-sCMGE after DNA replication initiation
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8p62
Q-score: 0.382
Henrikus SS, Gross MH, Willhoft O, Puhringer T, Lewis JS, McClure AW, Greiwe JF, Palm G, Nans A, Diffley JFX, Costa A
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01280-z Pubmed: 38760633 ]
- Dna (9-mer) (Complex from synthetic construct)
- Dna replication licensing factor mcm3 (111 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 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 psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (25 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna (9-mer) (2 kDa, DNA from synthetic construct)
- Cell division control protein 45, and dna polymerase epsilon subunit a and b (Complex from Saccharomyces cerevisiae)
- Complex of mcm2-7, cdc45, gins (psf1-3, sld5) dna polymerase epsilon (subunit a and b), 9-mer dna molecule (Complex)
- Dna replication licensing factors mcm2-7 (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna replication complex gins containing psf1, psf2, psf3 and sld5 (Complex 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)
- Dna replication licensing factor mcm7 (95 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)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae consensus-sCMGE on ssDNA after DNA replication initiation
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8p63
Q-score: 0.4
Henrikus SS, Gross MH, Willhoft O, Puhringer T, Lewis JS, McClure AW, Greiwe JF, Palm G, Nans A, Diffley JFX, Costa A
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01280-z Pubmed: 38760633 ]
- Dna polymerase epsilon contains catalytic subunit a and non-catalytic subunit b (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (111 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 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 psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (25 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna (Complex from synthetic construct)
- Dna (9-mer) (2 kDa, DNA from synthetic construct)
- Dna replication licensing factors mcm2-7 (Complex from Saccharomyces cerevisiae)
- Complex of mcm2-7, cdc45, gins (psf1-3, sld5) dna polymerase epsilon (subunit a and b), 9-mer dna molecule (Complex)
- Magnesium ion (24 Da, Ligand)
- Dna replication complex gins containing psf1, psf2, psf3 and sld5 (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Cdc45 (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 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)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae sCMGE with N-ter Mcm10 density
Henrikus SS, Gross MH, Willhoft O, Puhringer T, Lewis JS, McClure AW, Greiwe JF, Palm G, Nans A, Diffley JFX, Costa A
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01280-z Pubmed: 38760633 ]
- Dna replication licensing factor mcm7 (Protein from DNA molecule)
- Dna polymerase epsilon contains catalytic subunit a and non-catalytic subunit b (Complex from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf1 (Protein from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 10 (Protein from Saccharomyces cerevisiae)
- Dna (Complex from DNA molecule)
- Dna replication licensing factor mcm4 (Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (Protein from Saccharomyces cerevisiae)
- Dna strand 1 (DNA from Saccharomyces cerevisiae)
- Dna replication licensing factors mcm2-7 (Complex from Saccharomyces cerevisiae)
- Dna replication complex gins containing psf1, psf2, psf3 and sld5 (Complex from Saccharomyces cerevisiae)
- Dna strand 2 (DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (Protein from Saccharomyces cerevisiae)
- Cdc45 (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm5 (Protein from Saccharomyces cerevisiae)
- Complex of mcm2-7, cdc45, gins (psf1-3, sld5) dna polymerase epsilon (subunit a and b), 19-mer dna molecule with complementary 7-mer dna molecule (Complex from Saccharomyces cerevisiae)
- Cell division control protein 45 (Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8w9d
Q-score: 0.263
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Unclear peptide (487 Da, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8w9e
Q-score: 0.188
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8w9f
Q-score: 0.156
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6n7w
Q-score: 0.324
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Dna-directed dna polymerase (79 kDa, Protein from Enterobacteria phage T7)
- Dna (25-mer) (7 kDa, DNA from Enterobacteria phage T7)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna (77-mer) (23 kDa, DNA from Enterobacteria phage T7)
- Trxa (11 kDa, Protein from Escherichia coli)
- D5ae7a mutant gp5 dna polymerase complexed with trx, fork dna, and incoming dttp (from gp4-gp5 leading-strand complexes) (Complex from Enterobacteria phage T7)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6n9u
Q-score: 0.477
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Gp5 dna polymerase and two gp4 primase subunits complexed with trx, rna/dna hybrid, and incoming dttp (from gp4-gp5 lagging-strand complex lags1) (Complex from Enterobacteria phage T7)
- Dna primase/helicase (62 kDa, Protein from Enterobacteria phage T7)
- Dna-directed dna polymerase (79 kDa, Protein from Enterobacteria phage T7)
- Dna (44-mer) (13 kDa, DNA from Enterobacteria phage T7)
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(*ap*cp*cp*ap*g)-d(p*(doc))-3') (1 kDa, RNA from Enterobacteria phage T7)
- Thymidine-5'-triphosphate (482 Da, Ligand)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6n9v
Q-score: 0.408
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Gp5 dna polymerase and two gp4 primase subunits complexed with trx, rna/dna hybrid, and incoming dttp (from gp4-gp5 lagging-strand complex lags1) (Complex from Enterobacteria phage T7)
- Dna primase/helicase (62 kDa, Protein from Enterobacteria phage T7)
- Primer (1 kDa, RNA from Enterobacteria phage T7)
- Template (13 kDa, DNA from Enterobacteria phage T7)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Dna-directed dna polymerase (79 kDa, Protein from Enterobacteria phage T7)