Cryo-EM structure of P97-VCPIP1 complex
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8yka
Q-score: 0.366
Liao T, Li R, Lu P, Liu Y, Yang R, Guo H, Wu Z, Wang R, Yuan L, Hu Z, Gao H, Li F
Adv Sci (2024) 11 pp. e2403417-e2403417 [ Pubmed: 39234822 DOI: doi:10.1002/advs.202403417 ]
- Transitional endoplasmic reticulum atpase (85 kDa, Protein from Homo sapiens)
- P97-vcpip1 complex (Complex from Homo sapiens)
- Deubiquitinating protein vcpip1 (63 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1038/s41467-024-52582-1 Pubmed: 39358329 ]
- De novo design mini-binder in complex with tcdb1 (Complex from Clostridioides difficile)
- Zinc ion (65 Da, Ligand)
- Toxin b (270 kDa, Protein from Clostridioides difficile)
- De novo design mini-binder (7 kDa, Protein from synthetic construct)
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 [ DOI: doi:10.1038/s41467-024-52582-1 Pubmed: 39358329 ]
- Zinc ion (65 Da, Ligand)
- Toxin b (270 kDa, Protein from Clostridioides difficile)
- Tcdb4 in complex with de novo design mini-binder (Complex from Clostridioides difficile)
- De novo design minibinder (7 kDa, Protein from synthetic construct)
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 [ 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)
- 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)
- E-rtc_rmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 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)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Primer (8 kDa, RNA 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 [ DOI: doi:10.1016/j.cell.2022.09.037 Pubmed: 36335936 ]
- E-rtc_mmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate) (420 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein 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)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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)
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)
Human OGT-OGA complex (conformation I)
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 ]
- Human ogt-oga complex (conformation i) (400 kDa, Complex from Homo sapiens)
Human OGT-OGA complex (Conformation III)
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 ]
- Human ogt-oga complex (conformation iii) (400 kDa, Complex from Homo sapiens)
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)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Protein o-glcnacase (103 kDa, Protein from Homo sapiens)
- Cryo-em structure of human ogt-oga complex (400 kDa, Complex from Homo sapiens)
- Udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (117 kDa, Protein from Homo sapiens)