Langya Virus G glycoprotein (LayV G) with stabilizing mutations
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8tvi
Q-score: 0.552
Wang Z, McCallum M, Yan L, Gibson CA, Sharkey W, Park YJ, Dang HV, Amaya M, Person A, Broder CC, Veesler D
PNAS (2024) 121 pp. e2314990121-e2314990121 [ DOI: doi:10.1073/pnas.2314990121 Pubmed: 38593070 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Langya virus attachment glycoprotein g (68 kDa, Protein from Langya virus)
- Stabilized langya virus attachment glycoprotein layvg (Complex from Langya virus)
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 ]
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_ump-nsp9 (350 kDa, Complex 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)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Uridine-5'-monophosphate (324 Da, Ligand)
- Water (18 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Replicase polyprotein 1ab (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Rna (25-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
lymphocytic choriomeningitis virus RNA-dependent RNA polymerase (LCMV-L protein)
lymphocytic choriomeningitis virus polymerase- Matrix Z Protein Complex (LCMV L-Z Complex)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7x6v
Q-score: 0.393
Liu L, Wang P, Liu A, Zhang L, Yan L, Guo Y, Xiao G, Rao Z, Lou Z
Protein Cell (2023) 14 pp. 703-707 [ Pubmed: 37038286 DOI: doi:10.1093/procel/pwad018 ]
- Manganese (ii) ion (54 Da, Ligand)
- Ring finger protein z (10 kDa, Protein from Lymphocytic choriomeningitis virus (strain Armstrong))
- Lcmv polymerase l protein (Complex from Lymphocytic choriomeningitis virus (strain Armstrong))
- Matrix protein z (Complex from Lymphocytic choriomeningitis virus (strain Armstrong))
- The complex of lcmv polymerase with matrix protein z (Complex)
- Zinc ion (65 Da, Ligand)
- Rna-directed rna polymerase l (254 kDa, Protein from Lymphocytic choriomeningitis virus (strain Armstrong))
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8gwf
Q-score: 0.29
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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- E-rtc_rna-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex)
- Nsp (Complex)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8gwg
Q-score: 0.007
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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Rna (Complex)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Protein from sars-cov-2 (Complex)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_smp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8gwi
Q-score: 0.185
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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (27-mer) (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_smp-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 8gwn
Q-score: 0.407
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)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_atmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7egq
Q-score: 0.384
Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2021) 184 pp. 3474-3485.e11 [ Pubmed: 34143953 DOI: doi:10.1016/j.cell.2021.05.033 ]
- Primer rna, template rna (Complex)
- Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp 7, 8, 9, 10, 12, 13, 14 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
Architecture of a SARS-CoV-2 mini replication and transcription complex
Resolution: 3.84 Å
EM Method: Single-particle
Fitted PDBs: 7cxn
Q-score: 0.367
Yan L, Zhang Y, Ge J, Zheng L, Gao Y, Wang T, Jia Z, Wang H, Huang Y, Li M, Wang Q, Rao Z, Lou Z
Nat Commun (2020) 11 pp. 5874-5874 [ DOI: doi:10.1038/s41467-020-19770-1 Pubmed: 33208736 ]
- Template rna (18 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Nsp7, nsp8, nsp12, nsp13 and rna (Complex)
- Rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*up*up*up*up*up*u)-3') (1 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Nsp7, nsp8, nsp12, nsp13 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)