The structure of ASFV DNA polymerase in replicating state
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8ywi
Q-score: 0.508
Kuai L, Sun J, Peng Q, Zhao X, Yuan B, Liu S, Bi Y, Shi Y
Nucleic Acids Res (2024) 52 pp. 10717-10729 [ Pubmed: 39189451 DOI: doi:10.1093/nar/gkae739 ]
- The primer strand (7 kDa, DNA from African swine fever virus)
- Dna polymerase (139 kDa, Protein from African swine fever virus)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- The template strand (11 kDa, DNA from African swine fever virus)
- The asfv dna polymerase in replicating state (Complex from African swine fever virus)
F-actin decorated by SipA497-669
Resolution: 2.7 Å
EM Method: Helical reconstruction
Fitted PDBs: 8c4c
Q-score: 0.648
Yuan B, Scholz J, Wald J, Thuenauer R, Hennell James R, Ellenberg I, Windhorst S, Faix J, Marlovits TC
Sci Adv (2023) 9 pp. eadj5777-eadj5777 [ DOI: doi:10.1126/sciadv.adj5777 Pubmed: 38064550 ]
- Phosphate ion (94 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cell invasion protein sipa (19 kDa, Protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)
- F-actin (Complex from Gallus gallus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin binding domain sipa497-669 (Complex from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)
- F-actin polymerized by sipa497-669 under low-salt conditions (Complex)
- Actin, alpha skeletal muscle (42 kDa, Protein from Gallus gallus)
F-actin decorated by SipA426-685
Resolution: 2.6 Å
EM Method: Helical reconstruction
Fitted PDBs: 8c4e
Q-score: 0.676
Yuan B, Scholz J, Wald J, Thuenauer R, Hennell James R, Ellenberg I, Windhorst S, Faix J, Marlovits TC
Sci Adv (2023) 9 pp. eadj5777-eadj5777 [ DOI: doi:10.1126/sciadv.adj5777 Pubmed: 38064550 ]
- Phosphate ion (94 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- F-actin (Complex from Gallus gallus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin binding domain sipa-c (Complex from Salmonella)
- Cell invasion protein sipa (28 kDa, Protein from Salmonella)
- F-actin polymerized by sipa497-669 under low-salt conditions (Complex)
- Actin, alpha skeletal muscle (42 kDa, Protein from Gallus gallus)
The structure of EBOV L-VP35-RNA complex
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 8jsl
Q-score: 0.547
Peng Q, Yuan B, Cheng J, Wang M, Gao S, Bai S, Zhao X, Qi J, Gao GF, Shi Y
Nature (2023) 622 pp. 603-610 [ DOI: doi:10.1038/s41586-023-06608-1 Pubmed: 37699521 ]
- The leader sequence of ebov (5 kDa, RNA from Ebola virus)
- Zinc ion (65 Da, Ligand)
- Rna-directed rna polymerase l (252 kDa, Protein from Ebola virus)
- The structure of ebov l-vp35-rna complex (Complex from Ebola virus)
- Polymerase cofactor vp35 (37 kDa, Protein from Ebola virus)
The structure of EBOV L-VP35-RNA complex (conformation 1)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8jsm
Q-score: 0.495
Peng Q, Yuan B, Cheng J, Wang M, Gao S, Bai S, Zhao X, Qi J, Gao GF, Shi Y
Nature (2023) 622 pp. 603-610 [ DOI: doi:10.1038/s41586-023-06608-1 Pubmed: 37699521 ]
- The leader sequence of ebov genome. (5 kDa, RNA from Ebola virus)
- Zinc ion (65 Da, Ligand)
- Rna-directed rna polymerase l (252 kDa, Protein from Ebola virus)
- The structure of ebov l-vp35-rna complex (conformation 1) (Complex from Ebola virus)
- Polymerase cofactor vp35 (37 kDa, Protein from Ebola virus)
The structure of EBOV L-VP35-RNA complex (conformation 2)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8jsn
Q-score: 0.475
Peng Q, Yuan B, Cheng J, Wang M, Gao S, Bai S, Zhao X, Qi J, Gao GF, Shi Y
Nature (2023) 622 pp. 603-610 [ DOI: doi:10.1038/s41586-023-06608-1 Pubmed: 37699521 ]
- The structure of ebov l-vp35-rna complex (conformation 2) (Complex from Ebola virus)
- Zinc ion (65 Da, Ligand)
- Rna-directed rna polymerase l (252 kDa, Protein from Ebola virus)
- Polymerase cofactor vp35 (37 kDa, Protein from Ebola virus)
- The leader sequence of ebov genome (5 kDa, RNA from Ebola virus)
The structure of EBOV L-VP35 complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7yer
Q-score: 0.531
Yuan B, Peng Q, Cheng J, Wang M, Zhong J, Qi J, Gao GF, Shi Y
Nature (2022) 610 pp. 394-401 [ DOI: doi:10.1038/s41586-022-05271-2 Pubmed: 36171293 ]
- Rna-directed rna polymerase l (252 kDa, Protein from Ebola virus)
- The complex of ebov l-vp35 (Complex from Ebola virus)
- Polymerase cofactor vp35 (37 kDa, Protein from Ebola virus)
- Zinc ion (65 Da, Ligand)
The structure of EBOV L-VP35-RNA complex (state2)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7yes
Q-score: 0.49
Yuan B, Peng Q, Cheng J, Wang M, Zhong J, Qi J, Gao GF, Shi Y
Nature (2022) 610 pp. 394-401 [ DOI: doi:10.1038/s41586-022-05271-2 Pubmed: 36171293 ]
- Rna-directed rna polymerase l (252 kDa, Protein from Ebola virus)
- The complex of ebov l-vp35 (Complex from Ebola virus)
- Vp35 of ebov l-vp35 complex (37 kDa, Protein from Ebola virus)
- Zinc ion (65 Da, Ligand)
The structure of EBOV L-VP35 in complex with suramin
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7yet
Q-score: 0.45
Yuan B, Peng Q, Cheng J, Wang M, Zhong J, Qi J, Gao GF, Shi Y
Nature (2022) 610 pp. 394-401 [ DOI: doi:10.1038/s41586-022-05271-2 Pubmed: 36171293 ]
- 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfon ic acid (1 kDa, Ligand)
- Rna-directed rna polymerase l (252 kDa, Protein from Ebola virus)
- Polymerase cofactor vp35 (37 kDa, Protein from Ebola virus)
- The complex of ebov l-vp35-suramin (Complex from Ebola virus)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7ctt
Q-score: 0.478
Peng Q, Peng R, Yuan B, Wang M, Zhao J, Fu L, Qi J, Shi Y
Innovation (NY) (2021) 2 pp. 100080-100080 [ Pubmed: 33521757 DOI: doi:10.1016/j.xinn.2021.100080 ]
- Template-rna (5'-r(p*ap*cp*up*ap*gp*cp*up*up*cp*up*up*ap*gp*gp*ap*gp*ap*a)-3') (12 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Magnesium ion (24 Da, Ligand)
- The complex of favipiravir bound to core polymerase from sars-cov-2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- [[(2~{r},3~{s},4~{r},5~{r})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (529 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer-rna (5'-r(p*up*up*cp*up*cp*cp*up*ap*ap*gp*ap*ap*gp*cp*up*a)-3') (6 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)