Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8rmr
Q-score: 0.326
Arragain B, Krischuns T, Pelosse M, Drncova P, Blackledge M, Naffakh N, Cusack S
Nat Commun (2024) 15 pp. 6910-6910 [ Pubmed: 39160148 DOI: doi:10.1038/s41467-024-51007-3 ]
- Asymmetric dimer composed of one flupola/h7n9-4m replicase and one flupola/h7n9-4m encapsidase, bridged by human anp32a (Complex from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Polymerase acidic protein (82 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Polymerase basic protein 2 (89 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Magnesium ion (24 Da, Ligand)
- Acidic leucine-rich nuclear phosphoprotein 32 family member a (31 kDa, Protein from Homo sapiens)
- Rna-directed rna polymerase catalytic subunit (86 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
Arragain B, Krischuns T, Pelosse M, Drncova P, Blackledge M, Naffakh N, Cusack S
Nat Commun (2024) 15 pp. 6910-6910 [ Pubmed: 39160148 DOI: doi:10.1038/s41467-024-51007-3 ]
- Polymerase acidic protein (82 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Heterotrimeric complex (from the asymmetric dimer composed of one flupola/h7n9-4m replicase and one flupola/h7n9-4m encapsidase, bridged by human anp32a) (Complex from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Polymerase basic protein 2 (89 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Acidic leucine-rich nuclear phosphoprotein 32 family member a (31 kDa, Protein from Homo sapiens)
- Rna-directed rna polymerase catalytic subunit (86 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8pm0
Q-score: 0.546
Krischuns T, Arragain B, Isel C, Paisant S, Budt M, Wolff T, Cusack S, Naffakh N
Nat Commun (2024) 15 pp. 1064-1064 [ DOI: doi:10.1038/s41467-024-45205-2 Pubmed: 38316757 ]
- 51-mer vrna loop (v51_mut_s) (16 kDa, RNA from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Polymerase acidic protein (84 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Rna pol ii ctd 6 repeats (site 1a/2a) (4 kDa, Protein from Homo sapiens)
- Rna-directed rna polymerase catalytic subunit (86 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Polymerase basic protein 2 (89 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Magnesium ion (24 Da, Ligand)
- Influenza a/h7n9 polymerase in replicase-like conformation in pre-initiation state with pol ii ps5 ctd peptide mimic bound in site 1a/2a (Complex from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 8pnp
Q-score: 0.611
Krischuns T, Arragain B, Isel C, Paisant S, Budt M, Wolff T, Cusack S, Naffakh N
Nat Commun (2024) 15 pp. 1064-1064 [ DOI: doi:10.1038/s41467-024-45205-2 Pubmed: 38316757 ]
- 51-mer vrna loop (v51_mut_s) (16 kDa, RNA from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Rna pol ii ctd 6 repeats (site 1a/2a) (4 kDa, Protein from Homo sapiens)
- Polymerase acidic protein (84 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Polymerase basic protein 2 (89 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Rna-directed rna polymerase catalytic subunit (86 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Influenza a/h7n9 polymerase in replicase-like conformation in pre-initiation state with pol ii ps5 ctd peptide mimic bound in site 1a/2a (Complex from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Water (18 Da, Ligand)
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 8pnq
Q-score: 0.586
Krischuns T, Arragain B, Isel C, Paisant S, Budt M, Wolff T, Cusack S, Naffakh N
Nat Commun (2024) 15 pp. 1064-1064 [ DOI: doi:10.1038/s41467-024-45205-2 Pubmed: 38316757 ]
- 51-mer vrna loop (v51_mut_s) (16 kDa, RNA from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Rna pol ii ctd 6 repeats (site 1a/2a) (4 kDa, Protein from Homo sapiens)
- Polymerase acidic protein (84 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Polymerase basic protein 2 (89 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase catalytic subunit (86 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Influenza a/h7n9 polymerase in replicase-like conformation in pre-initiation state with pol ii ps5 ctd peptide mimic bound in site 1a/2a (Complex from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine (483 Da, Ligand)
- Replication product (10 kDa, RNA from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
Influenza A/H7N9 polymerase symmetric dimer bound to the promoter (PA K289A/C489R)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8poh
Q-score: 0.497
Krischuns T, Arragain B, Isel C, Paisant S, Budt M, Wolff T, Cusack S, Naffakh N
Nat Commun (2024) 15 pp. 1064-1064 [ DOI: doi:10.1038/s41467-024-45205-2 Pubmed: 38316757 ]
- 51-mer vrna loop (v51_mut_s) (16 kDa, RNA from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Polymerase acidic protein, rna-directed rna polymerase catalytic subunit and polymerase basic protein 2 (Complex from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- 51-mer vrna loop (v51_mut_s) (Complex from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Influenza a/h7n9 polymerase in replicase-like conformation in pre-initiation state with pol ii ps5 ctd peptide mimic bound in site 1a/2a (Complex)
- Rna-directed rna polymerase catalytic subunit (86 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Magnesium ion (24 Da, Ligand)
- Polymerase acidic protein (84 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
- Polymerase basic protein 2 (88 kDa, Protein from Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.31 Å
EM Method: Single-particle
Fitted PDBs: 8gw1
Q-score: 0.332
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- E-rtc_ump-nsp9 (350 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Uridine-5'-monophosphate (324 Da, Ligand)
- Replicase polyprotein 1ab (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Manganese (ii) ion (54 Da, Ligand)
- Rna (25-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
MERS-CoV Nsp1 protein bound to the Human 40S Ribosomal subunit
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8t4s
Q-score: 0.59
Devarkar SC, Vetick M, Balaji S, Lomakin IB, Yang L, Jin D, Gilbert WV, Chen S, Xiong Y
Cell Rep (2023) 42 pp. 113156-113156 [ DOI: doi:10.1016/j.celrep.2023.113156 Pubmed: 37733586 ]
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- Mers-cov nsp1 bound to human 40s ribosomal subunit (Complex from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- Fau ubiquitin-like and ribosomal protein s30 (14 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- Replicase polyprotein 1ab (21 kDa, Protein from Middle East respiratory syndrome-related coronavirus)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 18s rrna (602 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
Cryo-EM structure of the NS5-SLA complex
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8gzp
Q-score: 0.486
Osawa T, Aoki M, Ehara H, Sekine SI
Mol Cell (2023) 83 pp. 2781- [ DOI: doi:10.1016/j.molcel.2023.06.023 Pubmed: 37478848 ]
- Zinc ion (65 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Rna (54 kDa, RNA from synthetic construct)
- Mini-genome rna (Complex from synthetic construct)
- Rna replicase complex bound to the mini-genome rna (Complex from Dengue virus)
- Magnesium ion (24 Da, Ligand)
- Ns5 (Complex from Dengue virus)
- Genome polyprotein (104 kDa, Protein from Dengue virus)
Cryo-EM structure of the NS5-NS3-SLA complex
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8gzq
Q-score: 0.429
Osawa T, Aoki M, Ehara H, Sekine SI
Mol Cell (2023) 83 pp. 2781- [ DOI: doi:10.1016/j.molcel.2023.06.023 Pubmed: 37478848 ]
- Zinc ion (65 Da, Ligand)
- Ns3 (Complex from Dengue virus)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Rna (54 kDa, RNA from synthetic construct)
- Mini-genome rna (Complex from synthetic construct)
- Rna replicase complex bound to the mini-genome rna (Complex from Dengue virus)
- Genome polyprotein (74 kDa, Protein from Dengue virus)
- Ns5 (Complex from Dengue virus)
- Genome polyprotein (104 kDa, Protein from Dengue virus)