SAGA-TBP filtered to show the position of the DUB domain
Resolution: 20.0 Å
EM Method: Single-particle
Fitted PDBs: 6tbm
Q-score: 0.08
Papai G, Frechard A, Kolesnikova O, Crucifix C, Schultz P, Ben-Shem A
Nature (2020) 577 pp. 711-716 [ Pubmed: 31969704 DOI: doi:10.1038/s41586-020-1944-2 ]
- Saga complex (Complex from Komagataella phaffii GS115)
- Spt20 (59 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (17 kda) of tfiid and saga complexes, involved in rna polymerase ii transcription initiation (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Spt8 (34 kDa, Protein from Komagataella phaffii GS115)
- Subunit (61/68 kda) of tfiid and saga complexes (66 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit of the saga transcriptional regulatory complex, involved in proper assembly of the complex (136 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription and mrna export factor sus1 (11 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription initiation factor tfiid subunit 10 (23 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (90 kda) of tfiid and saga complexes (80 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (60 kda) of tfiid and saga complexes (54 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit of the saga and saga-like transcriptional regulatory complexes, interacts with spt15p to act (39 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Polyubiquitin-b (8 kDa, Protein from Homo sapiens)
- Saga component (Complex from Komagataella phaffii GS115)
- Water (18 Da, Ligand)
- Transcription-associated protein (438 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit of saga histone acetyltransferase complex (79 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcriptional regulator involved in glucose repression of gal4p-regulated genes (81 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Tata-box binding protein (tbp) (27 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Tata-box binding protein (tbp) (Complex from Komagataella phaffii GS115)
- Saga-associated factor 11 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcriptional coactivator hfi1/ada1 (49 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Ubiquitin carboxyl-terminal hydrolase (56 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Saga bound to tbp (1 MDa, Complex)
- Polyubiquitin-b (Complex from Homo sapiens)
Cryo-EM structure of E. coli RNA polymerase elongation complex bound to CTP substrate
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6rh3
Q-score: 0.473
Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A
Mol Cell (2019) 75 pp. 298-309.e4 [ Pubmed: 31103420 DOI: doi:10.1016/j.molcel.2019.04.029 ]
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Cryo-em structure of e. coli rna polymerase elongation complex bound to ctp substrate (Complex)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Template dna (11 kDa, DNA from Escherichia coli K-12)
- Rna polymerase (Complex from Escherichia coli K-12)
- Rna (4 kDa, RNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Non-template dna (12 kDa, DNA from Escherichia coli K-12)
- Cytidine-5'-triphosphate (483 Da, Ligand)
- Nucleic acids (Complex from Escherichia coli K-12)
Cryo-EM structure of E. coli RNA polymerase elongation complex bound to GreB transcription factor
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6ri7
Q-score: 0.369
Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A
Mol Cell (2019) 75 pp. 298-309.e4 [ Pubmed: 31103420 DOI: doi:10.1016/j.molcel.2019.04.029 ]
- Rna polymerase elongation complex (Complex from Escherichia coli K-12)
- Rna (4 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Template dna (11 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Nucleic acid (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Greb (Complex from Escherichia coli)
- Transcription elongation factor greb (18 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Cryo-em structure of e. coli rna polymerase elongation complex bound to greb transcription factor (Complex)
Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex in non-swiveled state
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6ri9
Q-score: 0.425
Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A
Mol Cell (2019) 75 pp. 298-309.e4 [ Pubmed: 31103420 DOI: doi:10.1016/j.molcel.2019.04.029 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Non-template dna (11 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Cryo-em structure of e. coli rna polymerase backtracked elongation complex in non-swiveled state (Complex)
- Template dna (12 kDa, DNA from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli K-12)
- Nucleic acids (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna (4 kDa, RNA from Escherichia coli)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6rin
Q-score: 0.415
Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A
Mol Cell (2019) 75 pp. 298-309.e4 [ Pubmed: 31103420 DOI: doi:10.1016/j.molcel.2019.04.029 ]
- Zinc ion (65 Da, Ligand)
- Rna polymerase and greb (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Non-template dna (11 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Cryo-em structure of e. coli rna polymerase backtracked elongation complex bound to greb transcription factor (Complex)
- Template dna (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Nucleic acids (Complex from Escherichia coli K-12)
- Transcription elongation factor greb (18 kDa, Protein from Escherichia coli K12)
- Rna (4 kDa, RNA from Escherichia coli)
Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex in swiveled state
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6rip
Q-score: 0.456
Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A
Mol Cell (2019) 75 pp. 298-309.e4 [ Pubmed: 31103420 DOI: doi:10.1016/j.molcel.2019.04.029 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Non-template dna (11 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Template dna (12 kDa, DNA from Escherichia coli)
- Rna polymerase (Complex from Escherichia coli K-12)
- Nucleic acids (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Rna (4 kDa, RNA from Escherichia coli)
- Cryo-em structure of e. coli rna polymerase backtracked elongation complex in swiveled state (Complex)
CryoEM structure of E.coli RNA polymerase paused elongation complex bound to NusA
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6flq
Q-score: -0.011
Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A
Mol Cell (2018) 69 pp. 816-827.e4 [ DOI: doi:10.1016/j.molcel.2018.02.008 Pubmed: 29499136 ]
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(*cp*cp*up*gp*ap*up*cp*ap*gp*gp*cp*gp*ap*up*gp*up*gp*up*gp*cp*u)-3') (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Nucleic acids (Complex)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Transcription termination/antitermination protein nusa (54 kDa, Protein from Escherichia coli (strain K12))
- Dna (31-mer) (9 kDa, DNA from synthetic construct)
- Dna (39-mer) (11 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase, nusa (Complex from Escherichia coli K-12)
- Cryo-em structure of e. coli rna polymerase paused elongation complex bound to nusa (Complex)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6flp
Q-score: 0.334
Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A
Mol Cell (2018) 69 pp. 816-827.e4 [ DOI: doi:10.1016/j.molcel.2018.02.008 Pubmed: 29499136 ]
- Nucleic acids (Complex from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Cryo-em structure of e. coli rna polymerase paused elongation complex without rna hairpin bound to nusa (Complex)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna (30-mer) (9 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna (39-mer) (11 kDa, DNA from synthetic construct)
- Rna (5'-r(p*gp*ap*up*gp*up*gp*up*gp*cp*u)-3') (3 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase and nusa (Complex from Escherichia coli K-12)