Cryo-EM structure of Pyrococcus furiosus transcription elongation complex bound to Spt4/5
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8oki
Q-score: 0.48
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Nucleotide strands (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus rna polymerase (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna template strand (8 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Transcription elongation complex with spt4/5 (Complex)
- Dna non-template strand (7 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Rna (2 kDa, RNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Spt4/5 (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8p2i
Q-score: 0.461
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus apo form of rna polymerase open clamp conformation (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 kDa, Protein from Pyrococcus furiosus DSM 3638)
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 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 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)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 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)
- Rna polymerase ii subunit d (16 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 rpb3 (31 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna (32-mer) (9 kDa, DNA from unidentified)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna (41-mer) (12 kDa, DNA from unidentified)
- Rna polymerase ii subunit k (7 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 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 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)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Pol ii - tpase complex (Complex from Homo sapiens)
- 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)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 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 rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna (32-mer) (9 kDa, DNA from unidentified)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna (41-mer) (12 kDa, DNA from unidentified)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 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) 83 pp. 2464- [ DOI: doi:10.1016/j.molcel.2023.06.002 Pubmed: 37369200 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
- Dna (38-mer) (11 kDa, DNA from synthetic construct)
- Pol ii - tpase complex (Complex from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- 7n-methyl-8-hydroguanosine-5'-triphosphate (539 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 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 rpb3 (31 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Rna (29-mer) (9 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna (38-mer) (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- S-adenosylmethionine (398 Da, Ligand)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ DOI: doi:10.1016/j.molcel.2021.06.019 Pubmed: 34265249 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Dna and rna (Complex from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (Protein from Sus scrofa)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Rna polymerase (Complex from Sus scrofa)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
- Elongation and assocation factor (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Transcription elongation factor (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ DOI: doi:10.1016/j.molcel.2021.06.019 Pubmed: 34265249 ]
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from pig)
- Rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from pig)
- Rna polymerase ii subunit k (Protein from pig)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Dna and rna (Complex from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from pig)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from pig)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Elongation and association factor (Complex from Homo sapiens)
- Rna polymerase ii subunit g (Protein from pig)
- Dna-directed rna polymerase subunit beta (Protein from pig)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from pig)
- Rna polymerase ii subunit d (Protein from pig)
- Rna polymerase ii subunit f (Protein from pig)
- Transcription elongation factor (Complex from Homo sapiens)
- Rna polymerase ii subunit e (Protein from pig)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ DOI: doi:10.1016/j.molcel.2021.06.019 Pubmed: 34265249 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Elongation factors (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit beta (Protein from Sus scrofa)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna (Complex from HIV whole-genome vector AA1305#18)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ DOI: doi:10.1016/j.molcel.2021.06.019 Pubmed: 34265249 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Elongation factors (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (Protein from Sus scrofa)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Pig rna polymerase ii subunit k (Protein from Sus scrofa)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna (Complex from HIV whole-genome vector AA1305#18)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P
Mol Cell (2021) 81 pp. 3386-3399.e10 [ DOI: doi:10.1016/j.molcel.2021.06.019 Pubmed: 34265249 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Non-template dna (DNA from HIV whole-genome vector AA1305#18)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Rna (RNA from HIV whole-genome vector AA1305#18)
- Transcription elongation factor spt5 (Protein from Homo sapiens)
- Template dna (DNA from HIV whole-genome vector AA1305#18)
- Ell-associated factor 1 (Protein from Homo sapiens)
- Elongation factors (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Rna polymerase ii elongation factor ell2 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Transcription elongation factor spt4 (Protein from Homo sapiens)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit beta (Protein from Sus scrofa)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna (Complex from HIV whole-genome vector AA1305#18)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Transcription elongation complex of rna polymerase ii with elongation factors dsif, ell2 and eaf1 (Complex)