Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA2 conformation
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8var
Q-score: 0.422
Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA
J Biol Chem (2024) 300 pp. 107166-107166 [ DOI: doi:10.1016/j.jbc.2024.107166 Pubmed: 38490435 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna polymerase iii subunit tau (41 kDa, Protein from Escherichia coli)
- Dna polymerase iii subunit delta' (37 kDa, Protein from Escherichia coli)
- Dna (27-mer) (9 kDa, DNA from synthetic construct)
- Beta sliding clamp (40 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna polymerase iii subunit delta (38 kDa, Protein from Escherichia coli)
- Structure of the e. coli clamp loader bound to the beta clamp in an closed-dna2 conformation (Complex from Escherichia coli)
- Dna (5'-d(p*gp*cp*ap*gp*ap*cp*ap*cp*tp*ap*cp*gp*ap*gp*tp*ap*cp*ap*tp*a)-3') (6 kDa, DNA from synthetic construct)
MutSbeta bound to 61bp homoduplex DNA
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8oma
Q-score: 0.177
Lee J-H, Thomsen M, Daub H, Steinbacher S, Sztyler A, Thieulin-Pardo G, Neudegger T, Plotnikov N, Iyer RR, Wilkinson H, Monteagudo E, Felsenfeld DP, Haque T, Finley M, Dominguez C, Vogt TF, Prasad BC
To Be Published
- Mutsbeta bound to 61bp homoduplex dna (Complex from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna2 (5 kDa, DNA from Homo sapiens)
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Dna1 (5 kDa, DNA from Homo sapiens)
Type IIS Restriction Endonuclease PaqCI, DNA bound
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8epx
Q-score: 0.545
Kennedy MA, Hosford CJ, Azumaya CM, Luyten YA, Chen M, Morgan RD, Stoddard BL
Nucleic Acids Res (2023) 51 pp. 4467-4487 [ Pubmed: 36987874 DOI: doi:10.1093/nar/gkad228 ]
- Dna 1b (6 kDa, DNA from DNA molecule)
- Dna 2b (5 kDa, DNA from DNA molecule)
- Dna 3a (5 kDa, DNA from DNA molecule)
- Calcium ion (40 Da, Ligand)
- Dna 2a (4 kDa, DNA from DNA molecule)
- Dna 3b (5 kDa, DNA from DNA molecule)
- Type iis restriction endonuclease paqci (56 kDa, Protein from Paucibacter aquatile)
- Dna 4b (4 kDa, DNA from DNA molecule)
- Dna 1a (7 kDa, DNA from DNA molecule)
- Dna 4a (4 kDa, DNA from DNA molecule)
- Homotetramer paqci with associated dna duplexes (Complex from Paucibacter aquatile)
Consensus closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2)
Resolution: 2.14 Å
EM Method: Single-particle
Fitted PDBs: 8dr1
Q-score: 0.607
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ DOI: doi:10.7554/eLife.78253 Pubmed: 35939393 ]
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*a)-3') (4 kDa, DNA from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*cp*gp*gp*gp*gp*gp*g)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*cp*cp*cp*cp*tp*tp*t)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Consensus closed state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) (Complex from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8dr3
Q-score: 0.59
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ DOI: doi:10.7554/eLife.78253 Pubmed: 35939393 ]
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*a)-3') (4 kDa, DNA from Saccharomyces cerevisiae)
- Closed state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) with ntd (Complex from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*cp*gp*gp*gp*gp*gp*g)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*cp*cp*cp*cp*tp*tp*t)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD
Resolution: 2.45 Å
EM Method: Single-particle
Fitted PDBs: 8dr4
Q-score: 0.555
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ DOI: doi:10.7554/eLife.78253 Pubmed: 35939393 ]
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*cp*gp*gp*gp*gp*gp*g)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Open state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) without ntd (Complex from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*cp*cp*cp*cp*tp*tp*t)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*ap*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*g)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8dr5
Q-score: 0.508
Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK
eLife (2022) 11 [ DOI: doi:10.7554/eLife.78253 Pubmed: 35939393 ]
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna (5'-d(p*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*ap*gp*gp*gp*gp*gp*gp*gp*gp*gp*g)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Open state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) with ntd (Complex from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*cp*cp*cp*cp*cp*cp*cp*cp*cp*cp*tp*tp*t)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*c)-3') (4 kDa, DNA from Saccharomyces cerevisiae)
Closed linker DNA nucleosome reconstituted with GUB DNA
Arimura Y, Shih RM, Froom R, Funabiki H
Mol Cell (2021) 81 pp. 4377-4397.e12 [ Pubmed: 34478647 DOI: doi:10.1016/j.molcel.2021.08.010 ]
- H3.2 (Protein from Xenopus laevis)
- Gub dna (DNA from synthetic construct)
- H2a (Protein from Xenopus laevis)
- Closed linker dna nucleosome reconstituted with gub dna (Complex from Xenopus laevis)
- H4 (Protein from Xenopus laevis)
- Gub dna_2 (DNA from synthetic construct)
- H2b (Protein from Xenopus laevis)
Open linker DNA nucleosome reconstituted with GUB DNA
Arimura Y, Shih RM, Froom R, Funabiki H
Mol Cell (2021) 81 pp. 4377-4397.e12 [ Pubmed: 34478647 DOI: doi:10.1016/j.molcel.2021.08.010 ]
- Gub_dna_2 (DNA from synthetic construct)
- H3.2 (Protein from Xenopus laevis)
- Open linker dna nucleosome reconstituted with gub dna (Complex from Xenopus laevis)
- H2a (Protein from Xenopus laevis)
- H4 (Protein from Xenopus laevis)
- Gub_dna (DNA from synthetic construct)
- H2b (Protein from Xenopus laevis)