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 ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Swr1-complex protein 4 (64 kDa, Protein from Komagataella phaffii GS115)
- Actin (53 kDa, Protein from Komagataella phaffii GS115)
- Magnesium ion (24 Da, Ligand)
- Nua4 histone acetyltransferase complex (Complex from Komagataella phaffii GS115)
- Transcription-associated protein (438 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)
- Chromatin modification-related protein eaf1 (118 kDa, Protein from Komagataella phaffii GS115)
NuA4 Histone Acetyltransferase complex
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 ]
- Act1 (Protein from Komagataella phaffii GS115)
- Arp4 (Protein from Komagataella phaffii GS115)
- Tra1 (Protein from Komagataella phaffii GS115)
- Eaf1 (Protein from Komagataella phaffii GS115)
- Nua4 histone acetyltransferase complex (Complex from Komagataella phaffii GS115)
- Swc4 (Protein from Komagataella phaffii GS115)
- Epl1 (Protein from Komagataella phaffii GS115)
Cryo-EM structure of fatty acid synthase (FAS) from Pichia pastoris
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7bc4
Q-score: 0.551
Snowden JS, Alzahrani J, Sherry L, Stacey M, Rowlands DJ, Ranson NA, Stonehouse NJ
Sci Rep (2021) 11 pp. 9773-9773 [ Pubmed: 33963233 DOI: doi:10.1038/s41598-021-89196-2 ]
- Fatty acid synthase subunit alpha (206 kDa, Protein from Yeast)
- Fatty acid synthase (2 MDa, Complex from Komagataella phaffii GS115)
- Fatty acid synthase subunit beta (230 kDa, Protein from Yeast)
- Flavin mononucleotide (456 Da, Ligand)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7bc5
Q-score: 0.381
Snowden JS, Alzahrani J, Sherry L, Stacey M, Rowlands DJ, Ranson NA, Stonehouse NJ
Sci Rep (2021) 11 pp. 9773-9773 [ DOI: doi:10.1038/s41598-021-89196-2 Pubmed: 33963233 ]
- Fatty acid synthase (2 MDa, Complex from Komagataella phaffii GS115)
- Fatty acid synthase subunit alpha (206 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
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 ]
- Tata-box binding protein (tbp) (27 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))
- Saga component (Complex from Komagataella phaffii GS115)
- Polyubiquitin-b (8 kDa, Protein from Homo sapiens)
- Subunit (90 kda) of tfiid and saga complexes (80 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))
- Transcriptional coactivator hfi1/ada1 (49 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Saga-associated factor 11 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Spt20 (59 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))
- Ubiquitin carboxyl-terminal hydrolase (56 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))
- Saga complex (Complex from Komagataella phaffii GS115)
- Saga bound to tbp (1 MDa, Complex)
- Subunit of saga histone acetyltransferase complex (79 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Water (18 Da, Ligand)
- Transcription initiation factor tfiid subunit 10 (23 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))
- Tata-box binding protein (tbp) (Complex from Komagataella phaffii GS115)
- Spt8 (34 kDa, Protein from Komagataella phaffii GS115)
- Polyubiquitin-b (Complex from Homo sapiens)
- Subunit of the saga transcriptional regulatory complex, involved in proper assembly of the complex (136 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))
- Transcription-associated protein (438 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
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 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 (17 kda) of tfiid and saga complexes, involved in rna polymerase ii transcription initiation (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- 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)
- Tata-box binding protein (tbp) (26 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))
- Spt20 (59 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))
- Subunit of the saga transcriptional regulatory complex, involved in proper assembly of the complex (136 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Tata-box binding protein (tbp) (Complex from Komagataella phaffii GS115)
- Saga complex (Complex from Komagataella phaffii GS115)
- Subunit (61/68 kda) of tfiid and saga complexes (66 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))
- Saga bound to tbp (1 MDa, Complex)
- Transcription-associated protein (438 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Resolution: 7.9 Å
EM Method: Single-particle
Fitted PDBs: 6j4w
Q-score: 0.123
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI
Science (2019) 363 pp. 744-747 [ Pubmed: 30733384 DOI: doi:10.1126/science.aav8912 ]
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Rna polymerase subunit abc10-beta (8 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*gp*up*gp*up*up*up*gp*gp*gp*up*gp*gp*up*gp*gp*c)-3') (5 kDa, RNA from synthetic construct)
- Spt5 (101 kDa, Protein from Komagataella pastoris)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-5) of the nucleosome (Complex from Komagataella pastoris)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6j4x
Q-score: 0.233
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI
Science (2019) 363 pp. 744-747 [ Pubmed: 30733384 DOI: doi:10.1126/science.aav8912 ]
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Protein that forms a complex with spt4p (101 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*up*g)-3') (5 kDa, RNA from synthetic construct)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-1) of the nucleosome (intermediate conformation) (Complex from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6j4y
Q-score: 0.235
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI
Science (2019) 363 pp. 744-747 [ Pubmed: 30733384 DOI: doi:10.1126/science.aav8912 ]
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Protein that forms a complex with spt4p (101 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-1) of the nucleosome (+1b) (Complex from Komagataella phaffii)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna (5'-r(p*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*up*g)-3') (5 kDa, RNA from synthetic construct)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6j4z
Q-score: 0.244
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI
Science (2019) 363 pp. 744-747 [ Pubmed: 30733384 DOI: doi:10.1126/science.aav8912 ]
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Dna (42-mer) (12 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*gp*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*u)-3') (5 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase ii elongation complex bound with spt4/5 and foreign dna, stalled at shl(-1) of the nucleosome (Complex from Komagataella phaffii)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Spt5 (101 kDa, Protein from Komagataella pastoris)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))