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 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription and dna repair factor iih helicase subunit xpb (Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- Bulky dna lesion recognition complex 1 (270 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 3 (Protein from Homo sapiens)
- General transcription factor iih subunit 4 (Protein from Homo sapiens)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- Dna2 (DNA from synthetic construct)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- Centrin-2 (Protein from Homo sapiens)
- General transcription factor iih subunit 2 (Protein from Homo sapiens)
- General transcription factor iih subunit 1 (Protein from Homo sapiens)
Initial DNA-lesion (Cy5) binding by XPC and TFIIH
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8ebs
Q-score: 0.274
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription factor iih subunit 3 (34 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 4, p52 (52 kDa, Protein from Homo sapiens)
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 kDa, Protein from Homo sapiens)
- Bulky dna lesion recognition complex (580 kDa, Complex from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Dna (cy5) (16 kDa, DNA from synthetic construct)
- Calcium ion (40 Da, Ligand)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Dna (16 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6oen
Q-score: 0.322
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M
Nat Struct Mol Biol (2020) 27 pp. 119-126 [ DOI: doi:10.1038/s41594-019-0363-2 Pubmed: 32015552 ]
- Dna (57-mer) (18 kDa, DNA from Escherichia coli K-12)
- High mobility group protein b1 (18 kDa, Protein from Homo sapiens)
- V(d)j recombination-activating protein 1 (119 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Dna (57-mer) (18 kDa, DNA from Escherichia coli K-12)
- Dna (46-mer) (15 kDa, DNA from Escherichia coli K-12)
- Rag1/2 pre-reaction complex (dna1) (Complex from Mus musculus)
- Dna (46-mer) (15 kDa, DNA from Escherichia coli K-12)
- V(d)j recombination-activating protein 2 (59 kDa, Protein from Mus musculus)
Cryo-EM structure of mouse RAG1/2 12RSS-PRC/23RSS-NFC complex (DNA1)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6oeq
Q-score: 0.338
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 ]
- Dna (57-mer) (18 kDa, DNA from Escherichia coli K-12)
- Mouse rag1/2 12rss-prc/23rss-nfc complex (dna1) (Complex from Mus musculus)
- Dna (57-mer) (18 kDa, DNA from Escherichia coli K-12)
- Dna (46-mer) (15 kDa, DNA from Escherichia coli K-12)
- Dna (46-mer) (15 kDa, DNA from Escherichia coli K-12)
- Calcium ion (40 Da, Ligand)
- 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)
- Zinc ion (65 Da, Ligand)
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 6n7s
Q-score: 0.239
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Dna (25-mer) (7 kDa, DNA from Enterobacteria phage T7)
- Magnesium ion (24 Da, Ligand)
- Bacteriophage t7 gene product 4 (gp4) helicase primase dna complex ii (Complex from Enterobacteria phage T7)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Dna primase/helicase (62 kDa, Protein from Enterobacteria phage T7)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6n7w
Q-score: 0.324
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Dna (77-mer) (23 kDa, DNA from Enterobacteria phage T7)
- Dna (25-mer) (7 kDa, DNA from Enterobacteria phage T7)
- Magnesium ion (24 Da, Ligand)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- D5ae7a mutant gp5 dna polymerase complexed with trx, fork dna, and incoming dttp (from gp4-gp5 leading-strand complexes) (Complex from Enterobacteria phage T7)
- Trxa (11 kDa, Protein from Escherichia coli)
- Dna-directed dna polymerase (79 kDa, Protein from Enterobacteria phage T7)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6n9v
Q-score: 0.408
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Gp5 dna polymerase and two gp4 primase subunits complexed with trx, rna/dna hybrid, and incoming dttp (from gp4-gp5 lagging-strand complex lags1) (Complex from Enterobacteria phage T7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed dna polymerase (79 kDa, Protein from Enterobacteria phage T7)
- Template (13 kDa, DNA from Enterobacteria phage T7)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Dna primase/helicase (62 kDa, Protein from Enterobacteria phage T7)
- Primer (1 kDa, RNA from Enterobacteria phage T7)
- Zinc ion (65 Da, Ligand)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6n9w
Q-score: 0.334
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Gp5 dna polymerase binding to a and b subunits of gp4 primase-helicase hexamer complexed with trx, rna/dna hybrid, and incoming dttp (lags2) (Complex from Enterobacteria phage T7)
- Zinc ion (65 Da, Ligand)
- Template (13 kDa, DNA from Enterobacteria phage T7)
- Primer (1 kDa, RNA from Enterobacteria phage T7)
- Dna-directed dna polymerase (79 kDa, Protein from Enterobacteria phage T7)
- Magnesium ion (24 Da, Ligand)
- Dna primase/helicase (62 kDa, Protein from Enterobacteria phage T7)
- Thymidine-5'-triphosphate (482 Da, Ligand)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6n9x
Q-score: 0.371
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Gp5 dna polymerase binding to b and c subunits of gp4 primase-helicase hexamer complexed with trx, rna/dna hybrid, and incoming dttp (lags3) (Complex from Enterobacteria phage T7)
- Magnesium ion (24 Da, Ligand)
- Dna-directed dna polymerase (79 kDa, Protein from Enterobacteria phage T7)
- Template (13 kDa, DNA from Enterobacteria phage T7)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Dna primase/helicase (62 kDa, Protein from Enterobacteria phage T7)
- Primer (1 kDa, RNA from Enterobacteria phage T7)
- Zinc ion (65 Da, Ligand)