Complex structure of trailing EC of EC+EC (trailing EC-focused)
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 7mk9
Q-score: 0.317
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ DOI: doi:10.1016/j.molcel.2021.12.020 Pubmed: 35051353 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Rna (5'-r(p*up*cp*gp*ap*gp*ap*gp*gp*ap*up*cp*cp*cp*ap*a)-3') (4 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna (40-mer) (12 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Complex structure of trailing ec of the ec+ec (trailing ec -focused) (600 kDa, Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna (40-mer) (12 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 7mei
Q-score: 0.335
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ DOI: doi:10.1016/j.molcel.2021.12.020 Pubmed: 35051353 ]
- Dna (74-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna (74-mer) (22 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Rna (5'-r(p*up*cp*gp*ap*gp*ap*gp*gp*ap*up*cp*cp*cp*ap*a)-3') (4 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- Head-to-end colliding rnapii elongation (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(p*ap*ap*cp*up*ap*gp*up*up*ap*ap*gp*ap*gp*gp*up*u)-3') (5 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
RNA polymerase II pre-initiation complex (PIC1)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7ml0
Q-score: 0.417
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ DOI: doi:10.1016/j.molcel.2021.12.020 Pubmed: 35051353 ]
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna+tbp+tfiie+tfiif (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Non-template strand dna (20 kDa, DNA from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (58 kDa, Protein from Saccharomyces cerevisiae)
- Template strand dna (20 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Pol ii + tfiib (Complex from Saccharomyces cerevisiae)
- Rna polymerase ii pre-initiation complex (pic1) (Complex from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Tfiih (Complex from Saccharomyces cerevisiae)
RNA polymerase II pre-initiation complex (PIC2)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7ml1
Q-score: 0.291
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ DOI: doi:10.1016/j.molcel.2021.12.020 Pubmed: 35051353 ]
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Tfb1 (58 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Non-template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
- Pol ii + tfiib (Complex from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Dna+tfiia+tfiie+tfiif (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii pre-initiation complex (pic2) (Complex from Saccharomyces cerevisiae)
- Tfiih (Complex from Saccharomyces cerevisiae)
RNA polymerase II pre-initiation complex (PIC3)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ml2
Q-score: 0.241
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ DOI: doi:10.1016/j.molcel.2021.12.020 Pubmed: 35051353 ]
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii pre-initiation complex (pic3) (Complex from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Tfb1 (58 kDa, Protein from Saccharomyces cerevisiae)
- Tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih (52 kDa, Protein from Saccharomyces cerevisiae)
- Non-template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0004860.mrna.1.cds.1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Pol ii + tfiib (Complex from Saccharomyces cerevisiae)
- Template strand dna (17 kDa, DNA from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna+tbp+tfiia+tfiie+tfiif (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Tfiih (Complex from Saccharomyces cerevisiae)
General transcription factor TFIIH (weak binding)
Resolution: 7.6 Å
EM Method: Single-particle
Fitted PDBs: 7ml3
Q-score: 0.215
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ DOI: doi:10.1016/j.molcel.2021.12.020 Pubmed: 35051353 ]
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Tfb1 (58 kDa, Protein from Saccharomyces cerevisiae)
- General transcription factor tfiih (weak binding) (Complex from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Non-template strand dna (9 kDa, DNA from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih (52 kDa, Protein from Saccharomyces cerevisiae)
- Template strand dna (9 kDa, DNA from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Saccharomyces cerevisiae)
RNA polymerase II initially transcribing complex (ITC)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7ml4
Q-score: 0.281
Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K
Mol Cell (2022) 82 pp. 660-676.e9 [ DOI: doi:10.1016/j.molcel.2021.12.020 Pubmed: 35051353 ]
- Template strand dna (34 kDa, DNA from Saccharomyces cerevisiae)
- Transcription initiation factor iib (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Bj4_g0050160.mrna.1.cds.1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Tfb1 (58 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Pol ii + tfiib + rna (Complex from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit (191 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih (52 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunit beta (138 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases ii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i,ii,and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna+tbp+tfiia+tfiie+tfiif (Complex from Saccharomyces cerevisiae)
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Rna (1 kDa, RNA from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii initially transcribing complex (itc) (Complex from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases ii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Non-template strand dna (11 kDa, DNA from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (54 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Tfiih (Complex from Saccharomyces cerevisiae)
Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7k01
Q-score: 0.331
van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K
Nat Commun (2021) 12 pp. 3338-3338 [ Pubmed: 34099686 DOI: doi:10.1038/s41467-021-23684-x ]
- Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Dna repair helicase rad25 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Ternary complex of tfiih/rad4-rad23-rad33 with aaf damaged dna (420 MDa, Complex)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening
Resolution: 9.25 Å
EM Method: Single-particle
Fitted PDBs: 7k04
Q-score: 0.122
van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K
Nat Commun (2021) 12 pp. 3338-3338 [ Pubmed: 34099686 DOI: doi:10.1038/s41467-021-23684-x ]
- Damaged dna strand (8 kDa, DNA from synthetic construct)
- Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 10 component complex of rad4-23, rad33 and tfiih on damaged dna (Complex)
- Iron/sulfur cluster (351 Da, Ligand)
- Undamaged dna strand (8 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair protein rad4 (87 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair protein rad33 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad25 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Calcium ion (40 Da, Ligand)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 6xi8
Q-score: 0.185
van Eeuwen T, Li T, Kim HJ, Gorbea Colon JJ, Parker MI, Dunbrack RL, Garcia BA, Tsai KL, Murakami K
Sci Adv (2021) 7 [ DOI: doi:10.1126/sciadv.abd4420 Pubmed: 33827808 ]
- Cyclin ccl1 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Aluminum fluoride (83 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Serine/threonine-protein kinase kin28 (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ternary complex of kin28-ccl1-tfb3 from saccharomyces cerevisiae. (73 kDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 3 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))