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Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase
Resolution: 5.5 Å
EM Method: Single-particle
Fitted PDBs: 7oyg
Q-score: 0.151
Jochheim FA, Tegunov D, Hillen HS, Schmitzova J, Kokic G, Dienemann C, Cramer P
Communications Biology (2021) 4 pp. 999- [ DOI: doi:10.1038/s42003-021-02529-9 ]
- 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)
- Dimeric form of sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) (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 nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Zinc ion (65 Da, Ligand)
SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand base-paired with A
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7ozu
Q-score: 0.522
Kabinger F, Stiller C, Schmitzova J, Dienemann C, Kokic G, Hillen HS, Hobartner C, Cramer P
Nat Struct Mol Biol (2021) 28 pp. 740-746 [ DOI: doi:10.1038/s41594-021-00651-0 Pubmed: 34381216 ]
- Replicase polyprotein 1ab (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (10 kDa, RNA from synthetic construct)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Product rna (10 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rdrp (183 MDa, Complex)
- Non-structural protein 8 (24 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand base-paired with G
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7ozv
Q-score: 0.525
Kabinger F, Stiller C, Schmitzova J, Dienemann C, Kokic G, Hillen HS, Hobartner C, Cramer P
Nat Struct Mol Biol (2021) 28 pp. 740-746 [ DOI: doi:10.1038/s41594-021-00651-0 Pubmed: 34381216 ]
- Replicase polyprotein 1ab (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (10 kDa, RNA from synthetic construct)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Rdrp (183 MDa, Complex)
- Product rna (10 kDa, RNA from synthetic construct)
- Non-structural protein 8 (24 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7b3b
Q-score: 0.501
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 ]
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing remdesivir at position -3. (Complex)
- Rna (5'-r(p*up*gp*cp*ap*up*cp*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)
- Dna/rna (5'-r(p*cp*up*ap*cp*gp*cp*g)-d(p*(rmp))-r(p*up*g)-3') (4 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 nsp7 and nsp8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7b3c
Q-score: 0.455
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 ]
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Dna/rna (5'-r(p*cp*up*ap*cp*gp*cp*a)-d(p*(rmp))-r(p*gp*up*g)-3') (4 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)
- Rna (5'-r(p*up*cp*ap*cp*up*up*gp*cp*gp*up*ap*g)-3') (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 nsp7 and 8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing remdesivir at position -4. (Complex)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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 ]
- 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 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex 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)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 rna-dependent rna polymerase nsp12 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 and 8 (Complex 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 rna-dependent rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6ted
Q-score: 0.338
Vos SM, Farnung L, Linden A, Urlaub H, Cramer P
Nat Struct Mol Biol (2020) 27 pp. 668-677 [ DOI: doi:10.1038/s41594-020-0437-1 Pubmed: 32541898 ]
- Rna polymerase ii subunit d (16 kDa, Protein from Pig)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Pig)
- Dna (37-mer) (14 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit f (14 kDa, Protein from Pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Pig)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Pig)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit g (19 kDa, Protein from Pig)
- Dna/rna (Complex from synthetic construct)
- Uncharacterized protein (7 kDa, Protein from Pig)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit c (31 kDa, Protein from Pig)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Pig)
- Rna (5'-r(p*up*ap*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (14 kDa, RNA from synthetic construct)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Uncharacterized protein (13 kDa, Protein from Pig)
- Rna polymerase ii subunit e (24 kDa, Protein from Pig)
- Uncharacterized protein (7 kDa, Protein from Pig)
- Template dna (14 kDa, DNA from synthetic construct)
- Pig dna/rna polymerase subunits (Complex from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 and spt5 (Complex from Homo sapiens)
- Human transcription factors and associated proteins (Complex from Homo sapiens)
- Complete ec* (1 MDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
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-dependent rna polymerase complex consisting of nsp12, nsp8, nsp7 and duplex rna. (186 kDa, Complex)
- Duplex rna (Complex from synthetic construct)
- Nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna product (5 kDa, RNA from synthetic construct)
- Nsp8, nsp7 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Nsp12 (Complex from Severe acute respiratory syndrome coronavirus 2)
Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC3
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 5oik
Q-score: 0.373
Bernecky C, Plitzko JM, Cramer P
Nat Struct Mol Biol (2017) 24 pp. 809-815 [ Pubmed: 28892040 DOI: doi:10.1038/nsmb.3465 ]
- Rna polymerase ii (520 kDa, Complex from Bos taurus)
- Dna (43-mer) (13 kDa, DNA from synthetic construct)
- Rna polymerase ii-dsif elongation complex (690 kDa, Complex)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Bos taurus)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Uncharacterized protein (17 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Bos taurus)
- Dna-rna synthetic construct (40 kDa, Complex from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Bos taurus)
- Polymerase (rna) ii (dna directed) polypeptide d (16 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Bos taurus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Bos taurus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Bos taurus)
- Dna (43-mer) (13 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Bos taurus)
- Rna (5'-r(p*up*ap*up*ap*up*ap*cp*ap*up*ap*ap*ap*gp*ap*cp*cp*ap*gp*gp*c)-3') (16 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dsif (130 kDa, Complex from Homo sapiens)
RNA polymerase I initially transcribing complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 5n61
Q-score: 0.343
Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P
Cell (2017) 169 pp. 120-131.e22 [ DOI: doi:10.1016/j.cell.2017.03.003 Pubmed: 28340337 ]
- Rna polymerase i initially transcribing complex (950 kDa, Complex)
- Rna polymerase i-specific transcription initiation factor rrn3 (72 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa49 (46 kDa, Protein from Baker's yeast)
- Rna polymerase i-specific transcription initiation factor rrn7 (60 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa190 (186 kDa, Protein from Baker's yeast)
- Sulfate ion (96 Da, Ligand)
- Product rna (1 kDa, RNA from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn11 (59 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa43 (36 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa135 (135 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Baker's yeast)
- Rna polymerase i (590 kDa, Complex from Saccharomyces cerevisiae)
- Initial transcription dna/rna scaffold (60 kDa, Complex from Saccharomyces cerevisiae)
- Non-template dna (12 kDa, DNA from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn6 (102 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Baker's yeast)
- Dna-directed rna polymerase i subunit rpa14 (14 kDa, Protein from Baker's yeast)
- Core factor (220 kDa, Complex from Saccharomyces cerevisiae)
- Template dna (13 kDa, DNA from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa34 (26 kDa, Protein from Baker's yeast)
- Initiation factor rrn3 (70 kDa, Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Baker's yeast)