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Rpd3S bound to an H3K36Cme3 modified nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8tof
Q-score: 0.464
Nat Commun (2023) 14 pp. 8128-8128 [ Pubmed: 38065958 DOI: doi:10.1038/s41467-023-43968-8 ]
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Rco1 (515 Da, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Dna (176-mer) (63 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone n-terminal tail (657 Da, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Dna (176-mer) (66 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rpd3s bound to h3k36cme3 nucleosome (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
Structure of mammalian Pol II-TFIIS elongation complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8a40
Q-score: 0.486
Farnung L, Ochmann M, Garg G, Vos SM, Cramer P
Mol Cell (2022) 82 pp. 3126-3134.e7 [ Pubmed: 35858621 DOI: doi:10.1016/j.molcel.2022.06.027 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rna (4 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Template dna (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Mammalian pol ii-tfiis elongation complex (Complex from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
Structural insights into human co-transcriptional capping - structure 1
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8p4a
Q-score: 0.344
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ DOI: doi:10.1016/j.molcel.2023.06.002 Pubmed: 37369200 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*ap*ap*ap*ap*cp*cp*cp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (6 kDa, RNA from unidentified)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna (38-mer) (11 kDa, DNA from unidentified)
- Dna (29-mer) (8 kDa, DNA from unidentified)
Structural insights into human co-transcriptional capping - structure 2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8p4b
Q-score: 0.434
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ DOI: doi:10.1016/j.molcel.2023.06.002 Pubmed: 37369200 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*gp*up*ap*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (7 kDa, RNA from unidentified)
- Dna (5'-d(p*ap*gp*cp*gp*gp*cp*gp*gp*ap*gp*cp*cp*ap*gp*cp*ap*gp*gp*gp*ap*gp*cp*tp*g)-3') (7 kDa, DNA from unidentified)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Dna (35-mer) (10 kDa, DNA from unidentified)
Structural insights into human co-transcriptional capping - structure 3
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8p4c
Q-score: 0.297
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ DOI: doi:10.1016/j.molcel.2023.06.002 Pubmed: 37369200 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna (41-mer) (12 kDa, DNA from unidentified)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna (32-mer) (9 kDa, DNA from unidentified)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from unidentified)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
Structural insights into human co-transcriptional capping - structure 4
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8p4d
Q-score: 0.348
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) 83 pp. 2464-2477.e5 [ DOI: doi:10.1016/j.molcel.2023.06.002 Pubmed: 37369200 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna (41-mer) (12 kDa, DNA from unidentified)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna (32-mer) (9 kDa, DNA from unidentified)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (6 kDa, RNA from unidentified)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
Structural insights into human co-transcriptional capping - structure 5
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8p4e
Q-score: 0.297
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) [ DOI: doi:10.1016/j.molcel.2023.06.002 Pubmed: 37369200 ]
- Dna (35-mer) (10 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from pig)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
- Rna polymerase ii subunit d (16 kDa, Protein from pig)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from pig)
- Rna (5'-d(*(mgt))-r(p*gp*ap*cp*ap*up*ap*cp*ap*up*ap*ap*ap*gp*ap*cp*cp*ap*gp*gp*c)-3') (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from pig)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from pig)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from pig)
- Dna (26-mer) (8 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from pig)
- Rna polymerase ii subunit k (7 kDa, Protein from pig)
- Zinc ion (65 Da, Ligand)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
Structural insights into human co-transcriptional capping - structure 6
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8p4f
Q-score: 0.29
Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P
Mol Cell (2023) [ DOI: doi:10.1016/j.molcel.2023.06.002 Pubmed: 37369200 ]
- Rna (29-mer) (9 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from pig)
- 7n-methyl-8-hydroguanosine-5'-triphosphate (539 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from pig)
- Dna (38-mer) (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
- Rna polymerase ii subunit d (16 kDa, Protein from pig)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from pig)
- Dna (38-mer) (11 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from pig)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from pig)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from pig)
- Rna polymerase ii subunit k (7 kDa, Protein from pig)
- Zinc ion (65 Da, Ligand)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
SIRT6 bound to an H3K9Ac nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8f86
Q-score: 0.434
Wang ZA, Markert JW, Whedon SD, Yapa Abeywardana M, Lee K, Jiang H, Suarez C, Lin H, Farnung L, Cole PA
J Am Chem Soc (2023) 145 pp. 6811-6822 [ Pubmed: 36930461 DOI: doi:10.1021/jacs.2c13512 ]
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- [(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3ar,5r,6r,6ar)-6-hydroxytetrahydro-2h-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) (587 Da, Ligand)
- Sirt6 bound to h3k9ac (Complex)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Dna (148-mer) (57 kDa, DNA from synthetic construct)
- Dna (148-mer) (56 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Nad-dependent protein deacylase sirtuin-6 (39 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7unc
Q-score: 0.344
Filipovski M, Soffers JHM, Vos SM, Farnung L
Science (2022) 376 pp. 1313-1316 [ Pubmed: 35709268 DOI: doi:10.1126/science.abo3851 ]
- Rpb11 (13 kDa, Protein from Sus scrofa)
- Pol ii-dsif-spt6-paf1c-tfiis complex with rewrapped nucleosome (Complex)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (219 kDa, Protein from pig)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from pig)
- Rpb8 (17 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from pig)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Non-template dna (64 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from pig)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rna (5 kDa, RNA from synthetic construct)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from pig)
- Rna polymerase ii subunit k (7 kDa, Protein from pig)
- Rpol4c domain-containing protein (20 kDa, Protein from pig)
- Rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from pig)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)