Cryo-EM structure of coxsackievirus A16 empty particle in complex with Fab h1A6.2 (local refinement)
Zhu R, Wu Y, Huang Y, Jiang Y, Jiang Y, Zhang D, Sun H, Zhou Z, Zhou L, Weng S, Chen H, Chen X, Ning W, Zou Y, He M, Yang H, Deng W, Li Y, Chen Z, Ye X, Han J, Yin Z, Zhao H, Liu C, Que Y, Fang M, Yu H, Zhang J, Luo W, Li S, Zheng Q, Xu L, Xia N, Cheng T
Nat Microbiol (2024) 9 pp. 2939-2953 [ Pubmed: 39424982 DOI: doi:10.1038/s41564-024-01822-7 ]
- Coxsackievirus a16 (Virus from Coxsackievirus A16)
- The heavy chain of fab h1a6.2 (12 kDa, Protein from Mus musculus)
- Genome polyprotein (26 kDa, Protein from Coxsackievirus A16)
- The fab of h1a6.2 (Complex from Mus musculus)
- Genome polyprotein (27 kDa, Protein from Coxsackievirus A16)
- Coxsackievirus a16 empty particle in complex with fab h1a6.2 (Complex)
- Capsid protein vp1 (33 kDa, Protein from Coxsackievirus A16)
- The light chain of fab h1a6.2 (12 kDa, Protein from Mus musculus)
Cryo-EM structure of Coxsackievirus B1 A-particle in complex with nAb 8A10 (CVB1-A:8A10)
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 7x35
Q-score: 0.557
Zheng Q, Zhu R, Yin Z, Xu L, Sun H, Yu H, Wu Y, Jiang Y, Huang Q, Huang Y, Zhang D, Liu L, Yang H, He M, Zhou Z, Jiang Y, Chen Z, Zhao H, Que Y, Kong Z, Zhou L, Li T, Zhang J, Luo W, Gu Y, Cheng T, Li S, Xia N
Cell Host Microbe (2022) 30 pp. 1279-1294.e6 [ DOI: doi:10.1016/j.chom.2022.08.001 Pubmed: 36002016 ]
- Virion protein 1 (31 kDa, Protein from Coxsackievirus B1)
- Coxsackievirus b1 (Virus from Coxsackievirus B1)
- Vp2 (29 kDa, Protein from Coxsackievirus B1)
- 8a10 light chain (11 kDa, Protein from Mus musculus)
- Vp3 (26 kDa, Protein from Coxsackievirus B1)
- 8a10 heavy chain (13 kDa, Protein from Mus musculus)
Cryo-EM structure of the EfPiwi (N959K)-piRNA-target ternary complex
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7yfq
Q-score: 0.435
Li Z, Li Z, Zhang Y, Zhou L, Xu Q, Li L, Zeng L, Xue J, Niu H, Zhong J, Yu Q, Li D, Gui M, Huang Y, Tu S, Zhang Z, Song CQ, Wu J, Shen EZ
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01287-6 Pubmed: 38658622 ]
- Efpiwi(n959k)-pirna-16nt target (Complex)
- Magnesium ion (24 Da, Ligand)
- Efpiwi(n959k) (Complex from Ephydatia fluviatilis)
- Rna (5'-r(*up*cp*cp*ap*up*gp*up*up*gp*ap*up*gp*gp*up*ap*a)-3') (5 kDa, RNA from Homo sapiens)
- Pirna (7 kDa, RNA from Homo sapiens)
- Rna (Complex)
- Piwi (92 kDa, Protein from Ephydatia fluviatilis)
Cryo-EM structure of Hili in complex with piRNA
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7yfx
Q-score: 0.425
Li Z, Li Z, Zhang Y, Zhou L, Xu Q, Li L, Zeng L, Xue J, Niu H, Zhong J, Yu Q, Li D, Gui M, Huang Y, Tu S, Zhang Z, Song CQ, Wu J, Shen EZ
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01287-6 Pubmed: 38658622 ]
- Magnesium ion (24 Da, Ligand)
- Pirna (8 kDa, RNA from Homo sapiens)
- Hili (Complex from Homo sapiens)
- Hili-pirna (Complex)
- Piwi-like protein 2 (114 kDa, Protein from Homo sapiens)
- Pirna (Complex)
Cryo-EM structure of the Mili-piRNA- target ternary complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7yfy
Q-score: 0.406
Li Z, Li Z, Zhang Y, Zhou L, Xu Q, Li L, Zeng L, Xue J, Niu H, Zhong J, Yu Q, Li D, Gui M, Huang Y, Tu S, Zhang Z, Song CQ, Wu J, Shen EZ
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01287-6 Pubmed: 38658622 ]
- Magnesium ion (24 Da, Ligand)
- Pirna (8 kDa, RNA from Homo sapiens)
- Mili (Complex from Mus musculus)
- Piwi-like protein 2 (91 kDa, Protein from Mus musculus)
- Mili-pirna-15nt target (Complex)
- Rna (Complex)
- Rna (5'-r(p*cp*cp*ap*up*gp*up*up*gp*ap*up*gp*gp*up*ap*a)-3') (4 kDa, RNA from Homo sapiens)
Cryo-EM structure of the EfPiwi(N959K) in complex with piRNA
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7yg6
Q-score: 0.399
Li Z, Li Z, Zhang Y, Zhou L, Xu Q, Li L, Zeng L, Xue J, Niu H, Zhong J, Yu Q, Li D, Gui M, Huang Y, Tu S, Zhang Z, Song CQ, Wu J, Shen EZ
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01287-6 Pubmed: 38658622 ]
- Magnesium ion (24 Da, Ligand)
- Efpiwi(n959k)-pirna (Complex)
- Efpiwi(n959k) (Complex from Ephydatia fluviatilis)
- Pirna (Complex)
- Pirna (7 kDa, RNA from Homo sapiens)
- Piwi (92 kDa, Protein from Ephydatia fluviatilis)
Cryo-EM structure of the Mili in complex with piRNA
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7ygn
Q-score: 0.5
Li Z, Li Z, Zhang Y, Zhou L, Xu Q, Li L, Zeng L, Xue J, Niu H, Zhong J, Yu Q, Li D, Gui M, Huang Y, Tu S, Zhang Z, Song CQ, Wu J, Shen EZ
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01287-6 Pubmed: 38658622 ]
- Magnesium ion (24 Da, Ligand)
- Pirna (8 kDa, RNA from Homo sapiens)
- Mili-pirna (Complex)
- Piwi-like protein 2 (91 kDa, Protein from Mus musculus)
- Pirna (Complex)
- Mili (Complex from Mus musculus)
TBOA-bound GltPh RSMR mutant in IFS state
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 7ug0
Q-score: 0.596
Huang Y, Reddy KD, Bracken C, Qiu B, Zhan W, Eliezer D, Boudker O
J Am Chem Soc (2023) 145 pp. 8583-8592 [ DOI: doi:10.1021/jacs.3c01003 ]
- (3s)-3-(benzyloxy)-l-aspartic acid (239 Da, Ligand)
- Water (18 Da, Ligand)
- Glutamate transporter homolog (44 kDa, Protein from Pyrococcus horikoshii)
- Sodium ion (22 Da, Ligand)
- Rsmr mutant bound with na/tboa (44 MDa, Cellular component from Pyrococcus horikoshii)
Asp-bound GltPh RSMR mutant in IFS-A1 state
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 7ugd
Q-score: 0.534
Huang Y, Reddy KD, Bracken C, Qiu B, Zhan W, Eliezer D, Boudker O
J Am Chem Soc (2023) 145 pp. 8583-8592 [ DOI: doi:10.1021/jacs.3c01003 ]
- Aspartic acid (133 Da, Ligand)
- Glutamate transporter homolog (44 kDa, Protein from Pyrococcus horikoshii)
- Gltph (Complex from Pyrococcus horikoshii)
- Sodium ion (22 Da, Ligand)
TBOA-bound GltPh RSMR mutant in OFS state
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 7ugj
Q-score: 0.531
Huang Y, Reddy KD, Bracken C, Qiu B, Zhan W, Eliezer D, Boudker O
J Am Chem Soc (2023) 145 pp. 8583-8592 [ DOI: doi:10.1021/jacs.3c01003 ]
- (3s)-3-(benzyloxy)-l-aspartic acid (239 Da, Ligand)
- Tboa-bound gltph rsmr mutant in ofs state (Complex from Pyrococcus horikoshii)
- Sodium ion (22 Da, Ligand)
- Glutamate transporter homolog (44 kDa, Protein from Pyrococcus horikoshii)