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)
Cryo-EM structure of an anti-phage defense complex bound to AMPPNP and DNA at state 1
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 8xaw
Q-score: 0.553
An Q, Wang Y, Tian Z, Han J, Li J, Liao F, Yu F, Zhao H, Wen Y, Zhang H, Deng Z
Cell Res (2024) 34 pp. 545-555 [ Pubmed: 38834762 DOI: doi:10.1038/s41422-024-00981-w ]
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- S20dna1 (18 kDa, DNA from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- S20dna2 (18 kDa, DNA from Escherichia coli)
- Atp-binding protein (64 kDa, Protein from Escherichia coli)
- Duf4297 (46 kDa, Protein from Escherichia coli)
- Duf4297-hera-dna-state2 (Complex from Escherichia coli)
Cryo-EM structure of an anti-phage defense complex bound to AMPPNP and DNA at state 2
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8xax
Q-score: 0.516
An Q, Wang Y, Tian Z, Han J, Li J, Liao F, Yu F, Zhao H, Wen Y, Zhang H, Deng Z
Cell Res (2024) 34 pp. 545-555 [ Pubmed: 38834762 DOI: doi:10.1038/s41422-024-00981-w ]
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Duf4297-hera-dna state1 (Complex from Escherichia coli)
- S20dna1 (18 kDa, DNA from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- S20dna2 (18 kDa, DNA from Escherichia coli)
- Atp-binding protein (64 kDa, Protein from Escherichia coli)
- Duf4297 (46 kDa, Protein from Escherichia coli)
Bulky DNA lesion recognition complex 3
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ DOI: doi:10.1038/s41586-023-05959-z Pubmed: 37076618 ]
- General transcription factor iih subunit 2 (Protein from Homo sapiens)
- General transcription factor iih subunit 4 (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- Bulky dna lesion recognition complex 3 (440 kDa, Complex from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (Protein from Homo sapiens)
- General transcription factor iih subunit 1 (Protein from Homo sapiens)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- Dna2 (DNA from synthetic construct)
- General transcription factor iih subunit 3 (Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (Protein from Homo sapiens)
Initial DNA-lesion (Cy5) binding by XPC and TFIIH focused
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ DOI: doi:10.1038/s41586-023-05959-z Pubmed: 37076618 ]
- General transcription factor iih subunit 2 (Protein from Homo sapiens)
- General transcription factor iih subunit 4 (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- General transcription factor iih subunit 1 (Protein from Homo sapiens)
- Dna2 (DNA from synthetic construct)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- General transcription factor iih subunit 3 (Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (Protein from Homo sapiens)
- Bulky dna lesion recognition complex 1 (270 kDa, Complex from Homo sapiens)
- Centrin-2 (Protein from Homo sapiens)
XPC release from Core7-XPA-DNA (Cy5)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ebu
Q-score: 0.341
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ DOI: doi:10.1038/s41586-023-05959-z Pubmed: 37076618 ]
- Dna1 (7 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Bulky dna lesion recognition complex3 (Complex from Homo sapiens)
- Dna2 (7 kDa, DNA from synthetic construct)
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.7554/eLife.77469 Pubmed: 35829698 ]
- Magnesium ion (24 Da, Ligand)
- Template strand (12 kDa, DNA from synthetic construct)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Proliferating cell nuclear antigen (29 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Primer strand (6 kDa, DNA from synthetic construct)
- Rfc-pcna-dna1-dna2 (Complex)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Dsdna (Complex from synthetic construct)
- Replication factor c subunit 1 (95 kDa, Protein from Saccharomyces cerevisiae)
- Proteins (Complex from Saccharomyces cerevisiae)
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 ]
- Magnesium ion (24 Da, Ligand)
- Template strand (12 kDa, DNA from synthetic construct)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Proliferating cell nuclear antigen (29 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Primer strand (6 kDa, DNA from synthetic construct)
- Rfc-pcna-dna1-dna2 (Complex)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Dsdna (Complex from synthetic construct)
- Replication factor c subunit 1 (95 kDa, Protein from Saccharomyces cerevisiae)
- Proteins (Complex from Saccharomyces cerevisiae)
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 ]
- Magnesium ion (24 Da, Ligand)
- Template strand (12 kDa, DNA from synthetic construct)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Primer strand (6 kDa, DNA from synthetic construct)
- Rfc-pcna-dna1-dna2 (Complex)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Dsdna (Complex from synthetic construct)
- Replication factor c subunit 1 (95 kDa, Protein from Saccharomyces cerevisiae)
- Proteins (Complex from Saccharomyces cerevisiae)
Cryo-EM 3D map of S. cerevisiae clamp loader RFC bound to DNA
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7tfl
Q-score: 0.329
Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME
eLife (2022) 11 [ DOI: doi:10.7554/eLife.77469 Pubmed: 35829698 ]
- Magnesium ion (24 Da, Ligand)
- Template strand (12 kDa, DNA from synthetic construct)
- Replication factor c subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Replication factor c subunit 5 (39 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Replication factor c subunit 4 (36 kDa, Protein from Saccharomyces cerevisiae)
- Primer strand (6 kDa, DNA from synthetic construct)
- Rfc-pcna-dna1-dna2 (Complex)
- Replication factor c subunit 2 (39 kDa, Protein from Saccharomyces cerevisiae)
- Dsdna (Complex from synthetic construct)
- Replication factor c subunit 1 (95 kDa, Protein from Saccharomyces cerevisiae)
- Proteins (Complex from Saccharomyces cerevisiae)