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)
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)
Cryo-EM structure of mouse RAG1/2 NFC complex (DNA2)
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 6oer
Q-score: 0.464
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M
Nat Struct Mol Biol (2020) 27 pp. 119-126 [ Pubmed: 32015552 DOI: doi:10.1038/s41594-019-0363-2 ]
- V(d)j recombination-activating protein 1 (119 kDa, Protein from Mus musculus)
- V(d)j recombination-activating protein 2 (59 kDa, Protein from Mus musculus)
- Rag1/2 nick-forming complex (dna2) (Complex)
- Dna (57-mer) (18 kDa, DNA from Escherichia coli K-12)
- Calcium ion (40 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna (46-mer) (15 kDa, DNA from Escherichia coli K-12)
- Dna (57-mer) (18 kDa, DNA from Escherichia coli K-12)
- High mobility group protein b1 (18 kDa, Protein from Equus caballus)
- Dna (46-mer) (15 kDa, DNA from Escherichia coli K-12)