Cryo-EM structure of the human Tip60 complex
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8qr1
Q-score: 0.484
Li C, Smirnova E, Schnitzler C, Crucifix C, Concordet JP, Brion A, Poterszman A, Schultz P, Papai G, Ben-Shem A
Nature (2024) 635 pp. 764-769 [ Pubmed: 39260417 DOI: doi:10.1038/s41586-024-08011-w ]
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Dna methyltransferase 1-associated protein 1 (53 kDa, Protein from Homo sapiens)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- E1a-binding protein p400 (343 kDa, Protein from Homo sapiens)
- Enhancer of polycomb homolog 1 (93 kDa, Protein from Homo sapiens)
- Tip60 complex (Cell from Homo sapiens)
- Actin, cytoplasmic 1, n-terminally processed (41 kDa, Protein from Homo sapiens)
- Vacuolar protein sorting-associated protein 72 homolog (40 kDa, Protein from Homo sapiens)
TRRAP and EP400 in the human Tip60 complex - composite map
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8qri
Q-score: 0.349
Li C, Smirnova E, Schnitzler C, Crucifix C, Concordet JP, Brion A, Poterszman A, Schultz P, Papai G, Ben-Shem A
Nature (2024) 635 pp. 764-769 [ Pubmed: 39260417 DOI: doi:10.1038/s41586-024-08011-w ]
- Transformation/transcription domain-associated protein (438 kDa, Protein from Homo sapiens)
- E1a-binding protein p400 (343 kDa, Protein from Homo sapiens)
- Human tip60 complex (Complex from Homo sapiens)
NuA4 Histone Acetyltransferase Complex (Composite)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7zvw
Q-score: 0.309
Frechard A, Faux C, Hexnerova R, Crucifix C, Papai G, Smirnova E, McKeon C, Ping FLY, Helmlinger D, Schultz P, Ben-Shem A
Nat Struct Mol Biol (2023) 30 pp. 1337-1345 [ Pubmed: 37550452 DOI: doi:10.1038/s41594-023-01056-x ]
- Nua4 histone acetyltransferase complex (Complex from Komagataella phaffii GS115)
- Chromatin modification-related protein eaf1 (118 kDa, Protein from Komagataella phaffii GS115)
- Transcription-associated protein (438 kDa, Protein from Komagataella phaffii GS115)
- Actin (53 kDa, Protein from Komagataella phaffii GS115)
- Swr1-complex protein 4 (64 kDa, Protein from Komagataella phaffii GS115)
- Enhancer of polycomb-like protein (86 kDa, Protein from Komagataella phaffii GS115)
- Actin (41 kDa, Protein from Komagataella phaffii GS115)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
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)
SAGA bound to TBP - whole structure
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6tb4
Q-score: 0.231
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 ]
- Transcriptional coactivator hfi1/ada1 (49 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Saga-associated factor 73 (sgf73) (79 kDa, Protein from Komagataella phaffii GS115)
- Saga complex (Complex from Komagataella phaffii GS115)
- 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))
- 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))
- Transcription-associated protein (438 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (61/68 kda) of tfiid and saga complexes (66 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Saga bound to tbp (1 MDa, Complex)
- Tata-box binding protein (tbp) (Complex from Komagataella phaffii GS115)
- Tata-box binding protein (tbp) (26 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 initiation factor tfiid subunit 10 (23 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcriptional adapter 3 (ada3) (6 kDa, Protein from Komagataella phaffii GS115)
- 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))
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)