human Lig1-DNA-PCNA complex reconstituted in absence of ATP
Resolution: 4.58 Å
EM Method: Single-particle
Fitted PDBs: 7qnz
Q-score: 0.361
Blair K, Tehseen M, Raducanu VS, Shahid T, Lancey C, Rashid F, Creuhet R, Hamdan SM, De Biasio A
Nat Commun (2022) 13 pp. 7833-7833 [ Pubmed: 36539424 DOI: doi:10.1038/s41467-022-35475-z ]
- Dna ligase 1 (101 kDa, Protein from Homo sapiens)
- Adenosine monophosphate (347 Da, Ligand)
- Proliferating cell nuclear antigen (29 kDa, Protein from Homo sapiens)
- Oligo19ddc (5 kDa, DNA from synthetic construct)
- Oligo32 (9 kDa, DNA from synthetic construct)
- Human ligase holoenzyme without atp present (Complex from Homo sapiens)
- Oligo13p (3 kDa, DNA from synthetic construct)
complex of DNA ligase I and FEN1 on PCNA and DNA
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 7qo1
Q-score: 0.303
Blair K, Tehseen M, Raducanu VS, Shahid T, Lancey C, Rashid F, Creuhet R, Hamdan SM, De Biasio A
Nat Commun (2022) 13 pp. 7833-7833 [ Pubmed: 36539424 DOI: doi:10.1038/s41467-022-35475-z ]
- Complex of dna ligase i and fen1 on pcna and dna (Complex from Homo sapiens)
- Adenosine monophosphate (347 Da, Ligand)
- Proliferating cell nuclear antigen (29 kDa, Protein from Homo sapiens)
- Flap endonuclease 1 (42 kDa, Protein from Homo sapiens)
- Oligo19ddc (5 kDa, DNA from synthetic construct)
- Oligo32 (9 kDa, DNA from synthetic construct)
- Dna ligase 1 (84 kDa, Protein from Homo sapiens)
- Oligo13p (3 kDa, DNA from synthetic construct)
FEN1 holoenzyme with a nicked DNA substrate
Blair K, Tehseen M, Raducanu VS, Shahid T, Lancey C, Rashid F, Creuhet R, Hamdan SM, De Biasio A
Nat Commun (2022) 13 pp. 7833-7833 [ Pubmed: 36539424 DOI: doi:10.1038/s41467-022-35475-z ]
- Oligo19ddc, oligo13p and oligo32 (Complex from synthetic construct)
- Oligo13p (DNA from synthetic construct)
- Flap endonuclease i (Protein from Homo sapiens)
- Proliferating cell nuclear antigen and flap endonuclease i (Complex from Homo sapiens)
- Complex of fen1 with pcna and dna (Complex)
- Proliferating cell nuclear antigen (Protein from Homo sapiens)
- Oligo32 (DNA from synthetic construct)
- Oligo19ddc (DNA from synthetic construct)
Open conformation of the complex of DNA ligase I on PCNA and DNA in the presence of ATP
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 8b8t
Q-score: 0.42
Blair K, Tehseen M, Raducanu VS, Shahid T, Lancey C, Rashid F, Creuhet R, Hamdan SM, De Biasio A
Nat Commun (2022) 13 pp. 7833-7833 [ Pubmed: 36539424 DOI: doi:10.1038/s41467-022-35475-z ]
- Complex of dna ligase i on pcna and dna in the presence of atp (Complex from Homo sapiens)
- Dna ligase 1 (29 kDa, Protein from Homo sapiens)
- Proliferating cell nuclear antigen (28 kDa, Protein from Homo sapiens)
Cryo electron micrographs of Pol delta-DNA-PCNA giving rise to various PCNA tilt angles
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A
Nat Commun (2020) 11 [ DOI: 10.1038/s41467-020-14898-6 Pubmed: 32111820 ]
Image sets:
- Cryo-electron micrographs of Pol delta holoenzyme giving rise to different tilted conformers, collection 3
- Cryo-electron micrographs of Pol delta holoenzyme giving rise to different tilted conformers, collection 1
- Cryo-electron micrographs of Pol delta holoenzyme giving rise to different tilted conformers, collection 2
Cryo electron micrographs of Pol delta-PCNA-DNA-FEN1 sample
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A
Nat Commun (2020) 11 [ DOI: 10.1038/s41467-020-14898-6 Pubmed: 32111820 ]
Image sets:
Human polymerase delta holoenzyme Conformer 1
Resolution: 4.27 Å
EM Method: Single-particle
Fitted PDBs: 6s1m
Q-score: 0.239
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A
Nat Commun (2020) 11 pp. 1109-1109 [ DOI: doi:10.1038/s41467-020-14898-6 Pubmed: 32111820 ]
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Dna polymerase delta subunit 2 (51 kDa, Protein from Homo sapiens)
- Dna polymerase delta subunit 4 (16 kDa, Protein from Homo sapiens)
- Pold holoenzyme (Complex)
- Dna primer (7 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (29 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Proliferating cell nuclear antigen (Complex from Homo sapiens)
- Dna template (11 kDa, DNA from synthetic construct)
- Dna polymerase delta catalytic subunit (123 kDa, Protein from Homo sapiens)
- Human polymerase delta (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna polymerase delta subunit 3 (52 kDa, Protein from Homo sapiens)
Human polymerase delta holoenzyme Conformer 2
Resolution: 4.86 Å
EM Method: Single-particle
Fitted PDBs: 6s1n
Q-score: 0.162
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A
Nat Commun (2020) 11 pp. 1109-1109 [ DOI: doi:10.1038/s41467-020-14898-6 Pubmed: 32111820 ]
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Dna polymerase delta subunit 2 (51 kDa, Protein from Homo sapiens)
- Dna polymerase delta subunit 4 (16 kDa, Protein from Homo sapiens)
- Pold holoenzyme (Complex)
- Dna primer (7 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (29 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Proliferating cell nuclear antigen (Complex from Homo sapiens)
- Dna template (11 kDa, DNA from synthetic construct)
- Dna polymerase delta catalytic subunit (123 kDa, Protein from Homo sapiens)
- Human polymerase delta (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna polymerase delta subunit 3 (52 kDa, Protein from Homo sapiens)
Human polymerase delta holoenzyme Conformer 3
Resolution: 8.1 Å
EM Method: Single-particle
Fitted PDBs: 6s1o
Q-score: 0.094
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A
Nat Commun (2020) 11 pp. 1109-1109 [ DOI: doi:10.1038/s41467-020-14898-6 Pubmed: 32111820 ]
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Dna polymerase delta subunit 2 (51 kDa, Protein from Homo sapiens)
- Dna polymerase delta subunit 4 (16 kDa, Protein from Homo sapiens)
- Pold holoenzyme (Complex)
- Dna primer (7 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (29 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Proliferating cell nuclear antigen (Complex from Homo sapiens)
- Dna template (11 kDa, DNA from synthetic construct)
- Dna polymerase delta catalytic subunit (123 kDa, Protein from Homo sapiens)
- Human polymerase delta (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna polymerase delta subunit 3 (52 kDa, Protein from Homo sapiens)
Processive human polymerase delta holoenzyme
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 6tny
Q-score: 0.442
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A
Nat Commun (2020) 11 pp. 1109-1109 [ DOI: doi:10.1038/s41467-020-14898-6 Pubmed: 32111820 ]
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Dna polymerase delta subunit 2 (51 kDa, Protein from Homo sapiens)
- Dna primer (7 kDa, DNA from synthetic construct)
- Proliferating cell nuclear antigen (29 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Proliferating cell nuclear antigen (Complex from Homo sapiens)
- Dna template (11 kDa, DNA from synthetic construct)
- Dna polymerase delta catalytic subunit (123 kDa, Protein from Homo sapiens)
- Dna polymerase delta subunit 4 (16 kDa, Protein from Homo sapiens)
- Dna primer, template (Complex from synthetic construct)
- Toolbelt (Complex)
- Dna polymerase (Complex from Homo sapiens)
- Dna polymerase delta subunit 3 (52 kDa, Protein from Homo sapiens)