Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8xk3
Q-score: 0.567
Tao X, Ding H, Wu S, Wang F, Xu H, Li J, Zhai C, Li S, Chen K, Wu S, Liu Y, Ma L
Nucleic Acids Res (2024) 52 pp. 11895-11910 [ DOI: doi:10.1093/nar/gkae820 Pubmed: 39315697 ]
- Water (18 Da, Ligand)
- Kmago (85 kDa, Protein from Kurthia massiliensis)
- Manganese (ii) ion (54 Da, Ligand)
- Kmago (Complex from Kurthia massiliensis)
- Target dna-2 (2 kDa, DNA from Kurthia massiliensis)
- Target dna-1 (2 kDa, DNA from Kurthia massiliensis)
- Guide dna (5 kDa, DNA from Kurthia massiliensis)
(CAG)2 DNA-bound MutSbeta in open form with kinked MSH2 clamp
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8rz7
Q-score: 0.292
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
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna mismatch repair protein (Complex from Homo sapiens)
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Dna_1 (20 kDa, DNA from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
- Mutsbeta-dna-adp complex (Complex)
- Double stranded dna (Complex from Homo sapiens)
- Dna_2 (18 kDa, DNA from Homo sapiens)
Structure of V. cholerae DdmD in complex with ssDNA
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 9bf5
Q-score: 0.455
Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM
Cell (2024) 187 pp. 5253-5266.e16 [ DOI: doi:10.1016/j.cell.2024.07.028 Pubmed: 39173632 ]
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
- Dimeric complex of v. cholerae ddmd bound with ssdna (Complex from Vibrio cholerae)
- Ssdna1 (4 kDa, DNA from Vibrio cholerae)
- Ssdna2 (4 kDa, DNA from Vibrio cholerae)
MutSbeta bound to (CAG)2 DNA (open form)
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8om9
Q-score: 0.249
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
- Magnesium ion (24 Da, Ligand)
- Dna2 (6 kDa, DNA from Homo sapiens)
- Mutsbeta bound to (cag)2 dna (open form) (Complex from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
- Dna1 (8 kDa, DNA from Homo sapiens)
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
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Mutsbeta bound to 61bp homoduplex dna (Complex from Homo sapiens)
- Dna1 (5 kDa, DNA from Homo sapiens)
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Dna2 (5 kDa, DNA from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
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 ]
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 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)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Water (18 Da, Ligand)
- Replication factor c subunit 4 (36 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)
- Consensus closed state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) (Complex from Saccharomyces cerevisiae)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- 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)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 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)
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 ]
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 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)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Water (18 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Closed state of rfc:pcna bound to a 3' ss/dsdna junction (dna2) with ntd (Complex 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)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- 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)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 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)
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 ]
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 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)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Replication factor c subunit 4 (36 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)
- Replication factor c subunit 1 (101 kDa, Protein 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*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (5 kDa, DNA from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Proliferating cell nuclear antigen (30 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)
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 ]
- Dna (5'-d(p*gp*gp*cp*cp*cp*cp*cp*cp*cp*gp*gp*c)-3') (3 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Replication factor c subunit 3 (38 kDa, Protein 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 4 (36 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)
- Replication factor c subunit 1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 2 (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)
- Dna (5'-d(p*tp*tp*tp*cp*gp*gp*gp*gp*gp*gp*gp*cp*c)-3') (4 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)
Structure of the core TFIIH-XPA-DNA complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6ro4
Q-score: 0.449
Kokic G, Chernev A, Tegunov D, Dienemann C, Urlaub H, Cramer P
Nat Commun (2019) 10 pp. 2885-2885 [ DOI: doi:10.1038/s41467-019-10745-5 Pubmed: 31253769 ]
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Dna2 (15 kDa, DNA from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Core tfiih-xpa-dna complex (Complex)
- Dna1 (15 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Tfiih-xpa (Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)