Cryo-EM structure of the Rev1-Polzeta-DNA-dCTP complex
Resolution: 3.53 Å
EM Method: Single-particle
Fitted PDBs: 8tlq
Q-score: 0.471
Malik R, Johnson RE, Ubarretxena-Belandia I, Prakash L, Prakash S, Aggarwal AK
Nat Struct Mol Biol (2024) [ Pubmed: 38720088 DOI: doi:10.1038/s41594-024-01302-w ]
- Dna (30-mer) (9 kDa, DNA from DNA molecule)
- Dna polymerase zeta processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna repair protein rev1 (112 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase zeta catalytic subunit (177 kDa, Protein from Saccharomyces cerevisiae)
- Dna complex (Complex from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Dna polymerase delta subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase delta small subunit (55 kDa, Protein from Saccharomyces cerevisiae)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Calcium ion (40 Da, Ligand)
Cryo-EM structure of Rev1(deltaN)-Polzeta-DNA-dCTP complex
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8tlt
Q-score: 0.579
Malik R, Johnson RE, Ubarretxena-Belandia I, Prakash L, Prakash S, Aggarwal AK
Nat Struct Mol Biol (2024) [ Pubmed: 38720088 DOI: doi:10.1038/s41594-024-01302-w ]
- Iron/sulfur cluster (351 Da, Ligand)
- Dna complex (Complex)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*tp*cp*cp*cp*cp*tp*ap*c)-3') (3 kDa, DNA from synthetic construct)
- Water (18 Da, Ligand)
- Dna polymerase zeta catalytic subunit, dna polymerase zeta processivity subunit, dna polymerase delta small subunit, dna polymerase delta subunit 3, dna repair protein rev1 (Complex from Saccharomyces cerevisiae)
- Dna polymerase delta subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae)
- Dna repair protein rev1 (112 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(*tp*ap*ap*tp*gp*gp*tp*ap*gp*gp*gp*gp*ap*gp*gp*gp*ap*ap*t)-3') (6 kDa, DNA from synthetic construct)
- Calcium ion (40 Da, Ligand)
- Dna polymerase delta small subunit (55 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex)
- Dna polymerase zeta processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase zeta catalytic subunit (177 kDa, Protein from Saccharomyces cerevisiae)
Structure of DNA polymerase zeta with mismatched DNA
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 7s0t
Q-score: 0.495
Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK
Nat Commun (2022) 13 pp. 1050-1050 [ DOI: doi:10.1038/s41467-022-28644-7 Pubmed: 35217661 ]
- Structure of dna complex (Complex from Saccharomyces cerevisiae)
- Dna polymerase zeta processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna polymerase zeta catalytic subunit (177 kDa, Protein from Saccharomyces cerevisiae)
- Dna (30-mer) (9 kDa, DNA from synthetic construct)
- Water (18 Da, Ligand)
- Dna polymerase delta subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase delta small subunit (55 kDa, Protein from Saccharomyces cerevisiae)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Calcium ion (40 Da, Ligand)
Structure of yeast DNA Polymerase Zeta (apo)
Resolution: 4.11 Å
EM Method: Single-particle
Fitted PDBs: 7lxd
Q-score: 0.23
Du Truong C, Craig TA, Cui G, Botuyan MV, Serkasevich RA, Chan KY, Mer G, Chiu PL, Kumar R
J Biol Chem (2021) 297 pp. 100912-100912 [ DOI: doi:10.1016/j.jbc.2021.100912 Pubmed: 34174285 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Dna polymerase zeta catalytic subunit (173 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase delta small subunit (55 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase zeta (172 MDa, Complex from Saccharomyces cerevisiae S288C)
- Dna polymerase delta subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase zeta processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of DNA Polymerase Zeta (Apo)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6v8p
Q-score: 0.369
Malik R, Kopylov M, Gomez-Llorente Y, Jain R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK
Nat Struct Mol Biol (2020) 27 pp. 913-924 [ DOI: doi:10.1038/s41594-020-0476-7 Pubmed: 32807989 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Apo (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase zeta processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase delta subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase zeta catalytic subunit (177 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase delta small subunit (55 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of DNA Polymerase Zeta/DNA/dNTP Ternary Complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6v93
Q-score: 0.539
Malik R, Kopylov M, Gomez-Llorente Y, Jain R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK
Nat Struct Mol Biol (2020) 27 pp. 913-924 [ Pubmed: 32807989 DOI: doi:10.1038/s41594-020-0476-7 ]
- Iron/sulfur cluster (351 Da, Ligand)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Dna polymerase zeta catalytic subunit (177 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Water (18 Da, Ligand)
- Structure of dna complex (Complex from Saccharomyces cerevisiae)
- Dna polymerase delta small subunit (55 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase delta subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Calcium ion (40 Da, Ligand)
- Dna polymerase zeta processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (9 kDa, DNA from synthetic construct)
Gomez-Llorente Y, Malik R, Jain R, Roy Choudhury J, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK
Cell Rep (2013) 5 pp. 79-86 [ Pubmed: 24120860 DOI: doi:10.1016/j.celrep.2013.08.046 ]
- Dna polymerase 'delta' subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase 'zeta' processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase 'zeta' catalytic subunit (173 kDa, Protein from Saccharomyces cerevisiae)
- Polymerase zeta heterotetramer of saccharomyces cerevisiae (300 kDa, Sample)
- Dna polymerase 'delta' small subunit (55 kDa, Protein from Saccharomyces cerevisiae)