Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9er2
Q-score: 0.448
van den Heuvel D, Rodriguez-Martinez M, van der Meer PJ, Nieto Moreno N, Park J, Kim HS, van Schie JJM, Wondergem AP, D'Souza A, Yakoub G, Herlihy AE, Kashyap K, Boissiere T, Walker J, Mitter R, Apelt K, de Lint K, Kirdok I, Ljungman M, Wolthuis RMF, Cramer P, Scharer OD, Kokic G, Svejstrup JQ, Luijsterburg MS
Cell (2024) 187 pp. 7107- [ DOI: doi:10.1016/j.cell.2024.10.018 Pubmed: 39547229 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase subunit (19 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 polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Nts (16 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Ts (15 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (218 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)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Isoform 1 of inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Pol ii-tcr-stk19 (Complex from Homo sapiens)
- Rna (5'-r(p*cp*ap*ap*ap*ap*up*cp*gp*ap*gp*ap*gp*gp*a)-3') (4 kDa, RNA from Homo sapiens)
- Transcription elongation factor 1 homolog (7 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
C(N)RL4CSA-UVSSA-E2-ubiquitin complex.
Kokic G, Yakoub G, van den Heuvel D, Wondergem AP, van der Meer PJ, van der Weegen Y, Chernev A, Fianu I, Fokkens TJ, Lorenz S, Urlaub H, Cramer P, Luijsterburg MS
Nat Struct Mol Biol (2024) 31 pp. 536-547 [ Pubmed: 38316879 DOI: doi:10.1038/s41594-023-01207-0 ]
- Cullin-4a (87 kDa, Protein from Homo sapiens)
- C(n)rl4csa-uvssa-e2-ubiquitin complex. (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Nedd8 (8 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d2 isoform x3 (16 kDa, Protein from Homo sapiens)
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 ]
- Sars-cov-2 nsp7 (9 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)
- 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)
- Zinc ion (65 Da, Ligand)
- 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: 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 ]
- Sars-cov-2 nsp7 and nsp8 (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)
- Non-structural protein 8 (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 remdesivir at position -3. (Complex)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- 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)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (Complex 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 ]
- 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)
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 and 8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein 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)
- 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 -4. (Complex)
- Sars-cov-2 rna-dependent rna polymerase (nsp12) (Complex 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 ]
- Sars-cov-2 rna-dependent rna polymerase nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 (9 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)
- Sars-cov-2 rna-dependent rna polymerase nsp12 (Complex 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 nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 nsp7 and 8 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Dna and rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 rna-dependent rna polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing amp at position -4. (Complex)
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)
- Zinc ion (65 Da, Ligand)
- Rna product (5 kDa, RNA from synthetic construct)
- Nsp8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp12 (107 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp8, nsp7 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Nsp12 (Complex from Severe acute respiratory syndrome coronavirus 2)
Structure of the core TFIIH-XPA-DNA complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6ro4
Q-score: 0.449
Kokic G, Chernev A, Tegunov D, Dienemann C, Urlaub H, Cramer P
Nat Commun (2019) 10 pp. 2885-2885 [ DOI: doi:10.1038/s41467-019-10745-5 Pubmed: 31253769 ]
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Dna2 (15 kDa, DNA from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Core tfiih-xpa-dna complex (Complex)
- Dna1 (15 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Tfiih-xpa (Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)