TcdB1 in complex with mini-binder
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8y9b
Q-score: 0.542
Lv X, Zhang Y, Sun K, Yang Q, Luo J, Tao L, Lu P
Nat Commun (2024) 15 pp. 8521-8521 [ Pubmed: 39358329 DOI: doi:10.1038/s41467-024-52582-1 ]
- De novo design mini-binder (7 kDa, Protein from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Toxin b (270 kDa, Protein from Clostridioides difficile)
- De novo design mini-binder in complex with tcdb1 (Complex from Clostridioides difficile)
De novo design mini-binder in complex with TcdB4
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8y9c
Q-score: 0.489
Lv X, Zhang Y, Sun K, Yang Q, Luo J, Tao L, Lu P
Nat Commun (2024) 15 pp. 8521-8521 [ Pubmed: 39358329 DOI: doi:10.1038/s41467-024-52582-1 ]
- Tcdb4 in complex with de novo design mini-binder (Complex from Clostridioides difficile)
- De novo design minibinder (7 kDa, Protein from synthetic construct)
- Toxin b (270 kDa, Protein from Clostridioides difficile)
- Zinc ion (65 Da, Ligand)
SARS-CoV-2 RNA E-RTC complex with RMP-nsp9 and GMPPNP
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 8gwk
Q-score: 0.423
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 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- E-rtc_rmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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 (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- [(2~{r},3~{s},4~{r},5~{r})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate (371 Da, Ligand)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 E-RTC bound with MMP-nsp9 and GMPPNP
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8gwm
Q-score: 0.41
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 ]
- Water (18 Da, Ligand)
- 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate) (420 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_mmp-nsp9_gmppnp (Complex 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)
- Rna (26-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 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: 3.31 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 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Uridine-5'-monophosphate (324 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- 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)
- Rna (25-mer) (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of human OGT-OGA complex
Resolution: 3.92 Å
EM Method: Single-particle
Fitted PDBs: 7yeh
Q-score: 0.269
Lu P, Liu Y, He M, Cao T, Yang M, Qi S, Yu H, Gao H
Nat Commun (2023) 14 pp. 6952-6952 [ DOI: doi:10.1038/s41467-023-42427-8 Pubmed: 37907462 ]
- Uridine-5'-diphosphate (404 Da, Ligand)
- Protein o-glcnacase (103 kDa, Protein from Homo sapiens)
- Udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (117 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cryo-em structure of human ogt-oga complex (400 kDa, Complex from Homo sapiens)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8gwe
Q-score: 0.019
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 ]
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Rna (5'-r(p*ap*up*up*a)-3') (1 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase nsp13 (65 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Zinc ion (65 Da, Ligand)
- E-rtc_rna-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Replicase polyprotein 1a (8 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 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: 3.39 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 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- 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)
- Zinc ion (65 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- E-rtc_rna-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp (Complex)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 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: 3.37 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 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Zinc ion (65 Da, Ligand)
- Protein from sars-cov-2 (Complex)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- E-rtc_smp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 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 ]
- E-rtc_smp-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
- Zinc ion (65 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Rna (27-mer) (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)