The RNA polymerase II elongation complex from Saccharomyces cerevisiae
Ma J, Yi G, Ye M, MacGregor-Chatwin C, Sheng Y, Lu Y, Li M, Li Q, Wang D, Gilbert RJC, Zhang P
Nat Commun (2024) 15 pp. 10304-10304 [ Pubmed: 39604363 DOI: doi:10.1038/s41467-024-53745-w ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*gp*gp*gp*ap*gp*ap*ap*gp*gp*ap*gp*c)-3') (22 kDa, DNA from synthetic construct)
- 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)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(p*gp*cp*tp*cp*cp*tp*tp*cp*tp*cp*cp*cp*ap*tp*cp*cp*tp*cp*tp*cp*gp*ap*t)-3') (22 kDa, DNA from synthetic construct)
- The rna polymerase ii elongation complex from saccharomyces cerevisiae (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Rna (5'-r(p*ap*up*cp*gp*ap*gp*ap*gp*g)-3') (2 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii (Complex)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna, rna (Complex)
Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8a3y
Q-score: 0.231
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 ]
- Mammalian pol ii-tfiis elongation complex (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein leo1 (210 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein rtf1 homolog (29 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (36 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Rna, template dna (9 kDa, RNA from synthetic construct)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna, template dna (42 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Non-template dna (39 kDa, DNA from synthetic construct)
- Spt6 (117 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
The closed state of the ASFV apo-RNA polymerase
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8q3b
Q-score: 0.54
Pilotto S, Sykora M, Cackett G, Dulson C, Werner F
Nat Commun (2024) 15 pp. 1606-1606 [ Pubmed: 38383525 DOI: doi:10.1038/s41467-024-45842-7 ]
- Dna-directed rna polymerase rpb10 homolog (9 kDa, Protein from African swine fever virus BA71V)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase rpb6 homolog (16 kDa, Protein from African swine fever virus BA71V)
- Uncharacterized protein c122r (11 kDa, Protein from African swine fever virus BA71V)
- Apo-form of the 8-subunit rna polymerase from african swine fever virus (450 kDa, Complex from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb5 homolog (23 kDa, Protein from African swine fever virus BA71V)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase rpb1 homolog (163 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb2 homolog (140 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb3-11 homolog (41 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb7 homolog (38 kDa, Protein from African swine fever virus BA71V)
The open state of the ASFV apo-RNA polymerase
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8q3k
Q-score: 0.531
Pilotto S, Sykora M, Cackett G, Dulson C, Werner F
Nat Commun (2024) 15 pp. 1606-1606 [ Pubmed: 38383525 DOI: doi:10.1038/s41467-024-45842-7 ]
- Dna-directed rna polymerase rpb10 homolog (9 kDa, Protein from African swine fever virus BA71V)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase rpb6 homolog (16 kDa, Protein from African swine fever virus BA71V)
- Uncharacterized protein c122r (11 kDa, Protein from African swine fever virus BA71V)
- Apo-form of the 8-subunit rna polymerase from african swine fever virus (450 kDa, Complex from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb5 homolog (23 kDa, Protein from African swine fever virus BA71V)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase rpb1 homolog (163 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb2 homolog (140 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb3-11 homolog (41 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb7 homolog (38 kDa, Protein from African swine fever virus BA71V)
Structure of the mammalian Pol II-SPT6 complex (composite map)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8oeu
Q-score: 0.526
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- The pol ii-spt6 transcription elongation complex (Complex from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- 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)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structure of the mammalian Pol II-SPT6-Elongin complex, lacking ELOA latch (composite map 2)
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8oev
Q-score: 0.468
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8oew
Q-score: 0.56
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- The pol ii-elongin transcription elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structure of the mammalian Pol II-SPT6-Elongin complex, Structure 1 (local resolution filtered map)
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8of0
Q-score: 0.422
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ DOI: doi:10.1038/s41594-023-01138-w Pubmed: 37932450 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (20 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
Structure of the Pol II-TCR-ELOF1 complex.
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8b3d
Q-score: 0.532
To Be Published
- Rpb7 (28 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Nts (16 kDa, DNA from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Rna (3 kDa, RNA from Homo sapiens)
- Ts (15 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa domesticus)
- Pol ii-tcr-elof1 complex. (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8b3f
Q-score: 0.456
To Be Published
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Pol ii-csb-csa-ddb1-elof1 complex. (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Nts (16 kDa, DNA from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Rna (3 kDa, RNA from Homo sapiens)
- Ts (15 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)