MPOX E5 hexamer 2ATP, 2ADP, and ssDNA binding comformation
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8wh2
Q-score: 0.516
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ DOI: doi:10.1126/sciadv.adl1150 Pubmed: 39167653 ]
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*cp*c)-3') (1 kDa, DNA from Spodoptera frugiperda)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Mpox helicase (Complex from Monkeypox virus)
MPOX E5 hexamer AMP-PNP and ssDNA bound form with clear primase domain
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8wgy
Q-score: 0.494
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ DOI: doi:10.1126/sciadv.adl1150 Pubmed: 39167653 ]
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Mpox helicase (Complex from Monkeypox virus)
- Dna (5'-d(p*cp*cp*c)-3') (822 Da, DNA from Spodoptera frugiperda)
MPOX E5 hexamer ssDNA and AMP-PNP bound conformation
Resolution: 2.51 Å
EM Method: Single-particle
Fitted PDBs: 8wh0
Q-score: 0.589
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ DOI: doi:10.1126/sciadv.adl1150 Pubmed: 39167653 ]
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*cp*c)-3') (1 kDa, DNA from Spodoptera frugiperda)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Mpox helicase (Complex from Monkeypox virus)
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8wh3
Q-score: 0.425
Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C
Sci Adv (2024) 10 pp. eadl1150-eadl1150 [ Pubmed: 39167653 DOI: doi:10.1126/sciadv.adl1150 ]
- Mpox helicase (Complex from Monkeypox virus)
- Uncoating factor opg117 (90 kDa, Protein from Monkeypox virus)
Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and dCTP
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8j8f
Q-score: 0.45
Xu Y, Wu Y, Wu X, Zhang Y, Yang Y, Li D, Yang B, Gao K, Zhang Z, Dong C
Int J Biol Macromol (2024) 270 pp. 132231-132231 [ DOI: doi:10.1016/j.ijbiomac.2024.132231 Pubmed: 38735603 ]
- Dna (5'-d(p*gp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*gp*ap*tp*ap*ap*cp*tp*tp*ap*ap*tp*cp*tp*cp*ap*cp*ap*tp*ap*gp*cp*ap*gp*cp*t)-3') (11 kDa, DNA from DNA molecule)
- Dna (5'-d(p*ap*gp*cp*tp*gp*cp*tp*ap*tp*gp*ap*gp*ap*tp*tp*ap*ap*gp*tp*tp*ap*t)-3') (7 kDa, DNA from DNA molecule)
- Monkeypox virus replication holoenzyme f8-a22-e4 in complex with a dna duplex and dctp (191 MDa, Complex from Monkeypox virus)
- E4r (27 kDa, Protein from Monkeypox virus)
- Dna polymerase processivity factor component a20 (49 kDa, Protein from Monkeypox virus)
- 2'-deoxycytidine-5'-triphosphate (467 Da, Ligand)
- Dna polymerase (120 kDa, Protein from Monkeypox virus)
- Calcium ion (40 Da, Ligand)
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8j8g
Q-score: 0.471
Xu Y, Wu Y, Wu X, Zhang Y, Yang Y, Li D, Yang B, Gao K, Zhang Z, Dong C
Int J Biol Macromol (2024) 270 pp. 132231-132231 [ DOI: doi:10.1016/j.ijbiomac.2024.132231 Pubmed: 38735603 ]
- Dna (5'-d(p*gp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*tp*gp*ap*tp*ap*ap*cp*tp*tp*ap*ap*tp*cp*tp*cp*ap*cp*ap*tp*ap*gp*cp*ap*gp*cp*t)-3') (11 kDa, DNA from DNA molecule)
- Dna (5'-d(p*ap*gp*cp*tp*gp*cp*tp*ap*tp*gp*ap*gp*ap*tp*tp*ap*ap*gp*tp*tp*ap*t)-3') (7 kDa, DNA from DNA molecule)
- Monkeypox virus replication holoenzyme f8-a22-e4 in complex with dna duplex and cidofovir diphosphate (191 MDa, Complex from Monkeypox virus)
- E4r (27 kDa, Protein from Monkeypox virus)
- Dna polymerase processivity factor component a20 (49 kDa, Protein from Monkeypox virus)
- [(2s)-1-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-propan-2-yl]oxymethyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphinic acid (439 Da, Ligand)
- Dna polymerase (120 kDa, Protein from Monkeypox virus)
- Calcium ion (40 Da, Ligand)
Rat Kir4.1 in complex with PIP2
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8i5m
Q-score: 0.486
Zhou X, Zhao C, Xu H, Xu Y, Zhan L, Wang P, He J, Lu T, Gu Y, Yang Y, Xu C, Chen Y, Liu Y, Zeng Y, Tian F, Chen Q, Xie X, Liu J, Hu H, Li J, Zheng Y, Guo J, Gao Z
Nat Chem Biol (2024) 20 pp. 857-866 [ Pubmed: 38355723 DOI: doi:10.1038/s41589-024-01555-y ]
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Atp-sensitive inward rectifier potassium channel 10 (38 kDa, Protein from Rattus norvegicus)
- Rat kir4.1 in complex with pip2 (Complex from Rattus norvegicus)
Rat Kir4.1 in complex with PIP2 and Lys05
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8i5n
Q-score: 0.414
Zhou X, Zhao C, Xu H, Xu Y, Zhan L, Wang P, He J, Lu T, Gu Y, Yang Y, Xu C, Chen Y, Liu Y, Zeng Y, Tian F, Chen Q, Xie X, Liu J, Hu H, Li J, Zheng Y, Guo J, Gao Z
Nat Chem Biol (2024) 20 pp. 857-866 [ Pubmed: 38355723 DOI: doi:10.1038/s41589-024-01555-y ]
- Rat kir4.1 in complex with pip2 and lys05 (Complex from Rattus norvegicus)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- Atp-sensitive inward rectifier potassium channel 10 (38 kDa, Protein from Rattus norvegicus)
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8hoy
Q-score: 0.292
Xu Y, Wu Y, Zhang Y, Fan R, Yang Y, Li D, Zhu S, Yang B, Zhang Z, Dong C
Cell Res (2023) 33 pp. 479-482 [ DOI: doi:10.1038/s41422-023-00796-1 Pubmed: 36973539 ]
- Monkeypox virus replication holoenzyme f8-a22-e4 complex without dna (191 MDa, Complex from Monkeypox virus)
- Dna polymerase (120 kDa, Protein from Monkeypox virus)
- E4r (27 kDa, Protein from Monkeypox virus)
- Dna polymerase processivity factor component a20 (49 kDa, Protein from Monkeypox virus)
Cryo-EM structure of the Omicron S in complex with 35B5 Fab(1 down-, 1 up- and 1 invisible RBDs)
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 7wlz
Q-score: 0.395
Wang X, Chen X, Tan J, Yue S, Zhou R, Xu Y, Lin Y, Yang Y, Zhou Y, Deng K, Chen Z, Ye L, Zhu Y
Cell Host Microbe (2022) 30 pp. 887- [ DOI: doi:10.1016/j.chom.2022.03.035 Pubmed: 35436443 ]
- Sars-cov-2 spike glycoprotein (Complex from Homo sapiens)
- Heavy chain of 35b5 fab (25 kDa, Protein from Homo sapiens)
- Complex of sars-cov-2 spike glycoprotein and 35b5 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 35b5 fab (Complex)
- Light chain of 35b5 fab (23 kDa, Protein from Homo sapiens)