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 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)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- 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)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (20 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)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (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 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)
- Elongin-c (12 kDa, Protein 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)
- The pol ii-elongin transcription elongation complex (Complex from Homo sapiens)
- Rna (14 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit d (20 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)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Elongin-a (90 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
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
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Pol ii-tcr-elof1 complex. (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Ts (15 kDa, DNA from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Nts (16 kDa, DNA from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rna (3 kDa, RNA from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Rpb7 (28 kDa, Protein from Sus scrofa domesticus)
Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7oob
Q-score: 0.566
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ Pubmed: 34526721 DOI: doi:10.1038/s41586-021-03906-4 ]
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rna (3 kDa, RNA 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 excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Complex between the transcribing rna polymerase ii and tcr factors in the presence of adp-bef3. (Complex)
- Dna excision repair protein ercc-6 and ercc-8, dna damage-binding protein 1 (Complex from Homo sapiens)
- 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)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Nts, rna, ts (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Beryllium trifluoride ion (66 Da, Ligand)
Pol II-CSB-CSA-DDB1-UVSSA (Structure1)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7oo3
Q-score: 0.521
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ Pubmed: 34526721 DOI: doi:10.1038/s41586-021-03906-4 ]
- Dna directed rna polymerase (Complex from Sus scrofa)
- Dna repair proteins, csb element and scaffold protein (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Rna (3 kDa, RNA 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)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Nts, ts & rna (Complex from Homo sapiens)
- Csb element (2 kDa, Protein from Homo sapiens)
- 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 polymerase ii elongation complex with csb, csa-ddb1 and uvssa. (Complex)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
Pol II-CSB-CSA-DDB1-UVSSA-PAF-SPT6 (Structure 3)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7oop
Q-score: 0.421
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ Pubmed: 34526721 DOI: doi:10.1038/s41586-021-03906-4 ]
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Complex between transcribing pol ii, tcr factors and elongation factors spt6 and paf. (Complex)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Supplementory proteins (Complex from Homo sapiens)
- 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)
- Rna (14 kDa, RNA from Homo sapiens)
- Rna polymerase-associated protein ctr9 homolog (133 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Nts, rna, ts (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Leo1 helix (3 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7b3d
Q-score: 0.558
Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P
Nat Commun (2021) 12 pp. 279-279 [ Pubmed: 33436624 DOI: doi:10.1038/s41467-020-20542-0 ]
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 rna-dependent rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*cp*up*ap*cp*gp*cp*ap*gp*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*up*gp*cp*ap*cp*up*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase nsp12 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing amp at position -4. (Complex)
- Sars-cov-2 nsp7 and 8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Structure of replicating SARS-CoV-2 polymerase
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6yyt
Q-score: 0.504
Hillen HS, Kokic G, Farnung L, Dienemann C, Tegunov D, Cramer P
Nature (2020) 584 pp. 154-156 [ DOI: doi:10.1038/s41586-020-2368-8 Pubmed: 32438371 ]
- Rna product (5 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna-dependent rna polymerase complex consisting of nsp12, nsp8, nsp7 and duplex rna. (186 kDa, Complex)
- Nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp12 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Duplex rna (Complex from synthetic construct)
- Nsp8, nsp7 (Complex from Severe acute respiratory syndrome coronavirus 2)