Electron Microscopy Data Bank

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Cryo-EM 3D map of the S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to two DNA molecules, one at the 5'-recessed end and the other at the 3'-recessed end

Release date: Nov. 16, 2022
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7tfh
Q-score: 0.469

Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME

eLife (2022) 11 [ Pubmed: 35829698 DOI: doi:10.7554/eLife.77469 ]

Sample:

Rfc-pcna-dna1-dna2 (Complex)
Dsdna (Complex from synthetic construct)
Replication factor c subunit 1 (95 kDa, Protein from Saccharomyces cerevisiae)
Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
Proteins (Complex from Saccharomyces cerevisiae)
Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
Proliferating cell nuclear antigen (29 kDa, Protein from Saccharomyces cerevisiae)
Template strand (12 kDa, DNA from synthetic construct)
Adenosine-5'-diphosphate (427 Da, Ligand)
Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
Magnesium ion (24 Da, Ligand)
Primer strand (6 kDa, DNA from synthetic construct)

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EMD-25873

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Cryo-EM 3D map of the S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to DNA with an open clamp

Release date: Nov. 16, 2022
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 7tfi
Q-score: 0.444

Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME

eLife (2022) 11 [ DOI: doi:10.7554/eLife.77469 Pubmed: 35829698 ]

Sample:

Dsdna (Complex from synthetic construct)
Replication factor c subunit 1 (95 kDa, Protein from Saccharomyces cerevisiae)
Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
Template strand (12 kDa, DNA from synthetic construct)
Adenosine-5'-diphosphate (427 Da, Ligand)
Proliferating cell nuclear antigen (29 kDa, Protein from Saccharomyces cerevisiae)
Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
Primer strand (6 kDa, DNA from synthetic construct)
Proteins (Complex from Saccharomyces cerevisiae)
Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
Rfc-pcna-dna1-dna2 (Complex)
Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)

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EMD-25874

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Cryo-EM 3D map of S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to DNA with a closed clamp ring

Release date: Nov. 16, 2022
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7tfj
Q-score: 0.458

Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME

eLife (2022) 11 [ DOI: doi:10.7554/eLife.77469 Pubmed: 35829698 ]

Sample:

Dsdna (Complex from synthetic construct)
Replication factor c subunit 1 (95 kDa, Protein from Saccharomyces cerevisiae)
Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
Template strand (12 kDa, DNA from synthetic construct)
Adenosine-5'-diphosphate (427 Da, Ligand)
Proliferating cell nuclear antigen (29 kDa, Protein from Saccharomyces cerevisiae)
Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
Primer strand (6 kDa, DNA from synthetic construct)
Proteins (Complex from Saccharomyces cerevisiae)
Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
Rfc-pcna-dna1 (Complex)

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EMD-25875

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Cryo-EM 3D map of S. cerevisiae clamp loader RFC bound to two DNA molecules, one at the 5'-recessed end and the other at the 3'-recessed end

Release date: Nov. 16, 2022
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 7tfk
Q-score: 0.39

Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME

eLife (2022) 11 [ DOI: doi:10.7554/eLife.77469 Pubmed: 35829698 ]

Sample:

Dsdna (Complex from synthetic construct)
Replication factor c subunit 1 (95 kDa, Protein from Saccharomyces cerevisiae)
Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
Template strand (12 kDa, DNA from synthetic construct)
Adenosine-5'-diphosphate (427 Da, Ligand)
Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
Primer strand (6 kDa, DNA from synthetic construct)
Proteins (Complex from Saccharomyces cerevisiae)
Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
Rfc-pcna-dna1-dna2 (Complex)
Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)

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EMD-21701

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Structure of the Saccharomyces cerevisiae polymerase epsilon holoenzyme

Release date: July 8, 2020
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6wjv
Q-score: 0.349

Yuan Z, Georgescu R, Schauer GD, O'Donnell ME, Li H

Nat Commun (2020) 11 pp. 3156- [ DOI: doi:10.1038/s41467-020-16910-5 ]

Sample:

Dna polymerase epsilon subunit d (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna polymerase epsilon subunit c (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna polymerase epsilon catalytic subunit a (255 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Zinc ion (65 Da, Ligand)
Dna polymerase epsilon (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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EMD-20607

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Structure of the S. cerevisiae replicative helicase CMG in complex with a forked DNA

Release date: March 25, 2020
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 ]

Sample:

Minichromosome maintenance protein 5 (74 kDa, Protein 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 mcm3 (79 kDa, Protein from Saccharomyces cerevisiae)
Cmg-forkdna (Complex from Saccharomyces cerevisiae)
Cell division control protein 45 (73 kDa, Protein from Saccharomyces cerevisiae)
Dna replication licensing factor mcm6 (73 kDa, Protein from Saccharomyces cerevisiae)
Adenosine-5'-triphosphate (507 Da, Ligand)
Dna replication licensing factor mcm7 (82 kDa, Protein from Saccharomyces cerevisiae)
Dna replication licensing factor mcm2 (74 kDa, Protein from Saccharomyces cerevisiae)
Dna (26-mer) (7 kDa, DNA from Saccharomyces cerevisiae)
Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
Dna replication complex gins protein psf2 (23 kDa, Protein from Saccharomyces cerevisiae)
Dna (15-mer) (4 kDa, DNA from Saccharomyces cerevisiae)
Dna replication licensing factor mcm4 (85 kDa, Protein from Saccharomyces cerevisiae)

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EMD-20473

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Structure of Ctf4 trimer in complex with three CMG helicases

Release date: Nov. 20, 2019
Resolution: 7.0 Å
EM Method: Single-particle
Fitted PDBs: 6pto
Q-score: 0.087

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 ]

Sample:

Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
Adenosine-5'-triphosphate (507 Da, Ligand)
Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
Cell division control protein 45 (74 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)
Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
Dna polymerase alpha-binding protein (104 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)
Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
Cmg-cmg-cmg-ctf4 (Complex from Saccharomyces cerevisiae)
Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)

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EMD-20471

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Structure of Ctf4 trimer in complex with one CMG helicase

Release date: Feb. 22, 2017
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 ]

Sample:

Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
Dna polymerase alpha-binding protein (104 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
Cmg-ctf4 (Complex from Saccharomyces cerevisiae)
Dna replication licensing factor mcm7 (95 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 psf2 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Minichromosome maintenance protein 5 (86 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)
Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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EMD-20472

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Structure of Ctf4 trimer in complex with two CMG helicases

Release date: Feb. 22, 2017
Resolution: 5.8 Å
EM Method: Single-particle
Fitted PDBs: 6ptn
Q-score: 0.087

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 ]

Sample:

Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
Adenosine-5'-triphosphate (507 Da, Ligand)
Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
Cmg-ctf4 (Complex from Saccharomyces cerevisiae)
Cell division control protein 45 (74 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)
Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae)
Dna polymerase alpha-binding protein (104 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)
Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)

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EMD-8519

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Structure of Eukaryotic CMG Helicase at a Replication Fork and Implications

Release date: Feb. 8, 2017
Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 5u8t
Q-score: 0.239

Georgescu R, Yuan Z, Bai L, de Luna Almeida Santos R, Sun J, Zhang D, Yurieva O, Li H, O'Donnell ME

PNAS (2017) 114 pp. E697-E706 [ Pubmed: 28096349 DOI: doi:10.1073/pnas.1620500114 ]

Sample:

Dna replication licensing factor mcm3 (107 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 complex gins protein psf3 (21 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 licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna (5'-d(p*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (4 kDa, DNA from Saccharomyces cerevisiae)
Cell division control protein 45 (74 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))
Cmg-ssdna (750 kDa, Complex from Saccharomyces cerevisiae)
Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
Minichromosome maintenance protein 5 (86 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna replication licensing factor mcm4 (105 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))
Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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