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 ]
- Replisome complex in state iv (1 MDa, Complex from Saccharomyces cerevisiae)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm6 (113 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 complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein sld5 (33 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 polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication complex gins protein psf3 (21 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 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)
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 [ Pubmed: 37730685 DOI: doi:10.1038/s41467-023-41506-0 ]
- 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)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm2 (98 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)
- Zinc ion (65 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)
- Dna replication licensing factor mcm7 (95 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 replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Replisome complex in state ii (1 MDa, Complex from Saccharomyces cerevisiae)
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 [ Pubmed: 37730685 DOI: doi:10.1038/s41467-023-41506-0 ]
- 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)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (70-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (25 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 replication complex gins protein sld5 (33 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 replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (61-mer) (18 kDa, DNA from Saccharomyces cerevisiae)
- Replisome complex in state ii (1 MDa, Complex from Saccharomyces cerevisiae)
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 [ Pubmed: 37730685 DOI: doi:10.1038/s41467-023-41506-0 ]
- Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Replisome complex in state v (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (71-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Zinc ion (65 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)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae S288C)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
Cryo-EM structure of yeast Erf2/Erf4 complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8hfc
Q-score: 0.503
Yang A, Liu S, Zhang Y, Chen J, Fan Y, Wang F, Zou Y, Feng S, Wu J, Hu Q
Nat Struct Mol Biol (2024) 31 pp. 436-446 [ Pubmed: 38182928 DOI: doi:10.1038/s41594-023-01183-5 ]
- Palmitic acid (256 Da, Ligand)
- Palmitoyltransferase erf2 (43 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ras modification protein erf4 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Erf2/erf4 complex (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
S. cerevisiae Chs1 in complex with polyoxin B
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 8k3p
Q-score: 0.437
Chen DD, Wang ZB, Wang LX, Zhao P, Yun CH, Bai L
Nat Commun (2023) 14 pp. 4776-4776 [ DOI: doi:10.1038/s41467-023-40479-4 Pubmed: 37553334 ]
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Chitin synthase 1 (133 kDa, Protein from Saccharomyces cerevisiae S288C)
- S. cerevisiae chs1 in complex with polyoxin b (Complex from Saccharomyces cerevisiae)
- (2s)-2-[[(2s,3s,4s)-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)pentanoyl]amino]-2-[(2r,3s,4r,5r)-5-[5-(hydroxymethyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethanoic acid (507 Da, Ligand)
Structure of Bre1-nucleosome complex - state1
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 8t3y
Q-score: 0.503
Nat Struct Mol Biol (2023) 30 pp. 1623-1627 [ DOI: doi:10.1038/s41594-023-01137-x Pubmed: 37872231 ]
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Bre1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase bre1 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b (13 kDa, Protein from Xenopus laevis)
CryoEM structure of the Dsl1 complex bound to SNAREs Sec20 and Use1
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 8eki
Q-score: 0.182
DAmico KA, Stanton AE, Shirkey JD, Travis SM, Jeffrey PD, Hughson FM
Nat Struct Mol Biol (2024) 31 pp. 246-254 [ Pubmed: 38196032 DOI: doi:10.1038/s41594-023-01164-8 ]
- Protein transport protein sec39 (82 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dsl1 complex (Complex from Saccharomyces cerevisiae)
- Protein transport protein sec20 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Protein transport protein dsl1 (91 kDa, Protein from Saccharomyces cerevisiae S288C)
- Protein transport protein use1 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- Protein transport protein tip20 (81 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dsl1 complex bound to snare proteins sec20 and use1 (255 kDa, Complex from Saccharomyces cerevisiae)