Cryo-EM reveals cholesterol binding in the lysosomal GPCR-like protein LYCHOS
Zhao J, Shen Q, Yong X, Li X, Tian X, Sun S, Xu Z, Zhang X, Zhang L, Yang H, Shao Z, Xu H, Jiang Y, Zhang Y, Yan W
Nat Struct Mol Biol (2025) [ Pubmed: 39824976 DOI: doi:10.1038/s41594-024-01470-9 ]
- Cholesterol-bound lychos (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Lysosomal cholesterol signaling protein (93 kDa, Protein from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- [(2r)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate (720 Da, Ligand)
- Cholesterol (386 Da, Ligand)
BA.2.86 RBD protein in complex with ACE2.
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8yzb
Q-score: 0.477
Liu Y, Zhao X, Shi J, Wang Y, Liu H, Hu YF, Hu B, Shuai H, Yuen TT, Chai Y, Liu F, Gong HR, Li J, Wang X, Jiang S, Zhang X, Zhang Y, Li X, Wang L, Hartnoll M, Zhu T, Hou Y, Huang X, Yoon C, Wang Y, He Y, Zhou M, Du L, Zhang X, Chan WM, Chen LL, Cai JP, Yuan S, Zhou J, Huang JD, Yuen KY, To KK, Chan JF, Zhang BZ, Sun L, Wang P, Chu H
Nat Commun (2024) 15 pp. 8728-8728 [ Pubmed: 39379369 DOI: doi:10.1038/s41467-024-53033-7 ]
- Spike glycoprotein,fibritin,fusion protein (142 kDa, Protein from synthetic construct)
- Ba.2.86 rbd protein in complex with ace2 (Complex from Homo sapiens)
- Angiotensin-converting enzyme 2 (85 kDa, Protein from Homo sapiens)
Structure of BA.2.86 spike protein in complex with ACE2.
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8yzc
Q-score: 0.267
Liu Y, Zhao X, Shi J, Wang Y, Liu H, Hu YF, Hu B, Shuai H, Yuen TT, Chai Y, Liu F, Gong HR, Li J, Wang X, Jiang S, Zhang X, Zhang Y, Li X, Wang L, Hartnoll M, Zhu T, Hou Y, Huang X, Yoon C, Wang Y, He Y, Zhou M, Du L, Zhang X, Chan WM, Chen LL, Cai JP, Yuan S, Zhou J, Huang JD, Yuen KY, To KK, Chan JF, Zhang BZ, Sun L, Wang P, Chu H
Nat Commun (2024) 15 pp. 8728-8728 [ Pubmed: 39379369 DOI: doi:10.1038/s41467-024-53033-7 ]
Structure of JN.1 RBD protein in complex with ACE2.
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8yzd
Q-score: 0.573
Liu Y, Zhao X, Shi J, Wang Y, Liu H, Hu YF, Hu B, Shuai H, Yuen TT, Chai Y, Liu F, Gong HR, Li J, Wang X, Jiang S, Zhang X, Zhang Y, Li X, Wang L, Hartnoll M, Zhu T, Hou Y, Huang X, Yoon C, Wang Y, He Y, Zhou M, Du L, Zhang X, Chan WM, Chen LL, Cai JP, Yuan S, Zhou J, Huang JD, Yuen KY, To KK, Chan JF, Zhang BZ, Sun L, Wang P, Chu H
Nat Commun (2024) 15 pp. 8728-8728 [ Pubmed: 39379369 DOI: doi:10.1038/s41467-024-53033-7 ]
The JN.1 spike protein (S) in complex with ACE2.
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8yze
Q-score: 0.25
Liu Y, Zhao X, Shi J, Wang Y, Liu H, Hu YF, Hu B, Shuai H, Yuen TT, Chai Y, Liu F, Gong HR, Li J, Wang X, Jiang S, Zhang X, Zhang Y, Li X, Wang L, Hartnoll M, Zhu T, Hou Y, Huang X, Yoon C, Wang Y, He Y, Zhou M, Du L, Zhang X, Chan WM, Chen LL, Cai JP, Yuan S, Zhou J, Huang JD, Yuen KY, To KK, Chan JF, Zhang BZ, Sun L, Wang P, Chu H
Nat Commun (2024) 15 pp. 8728-8728 [ Pubmed: 39379369 DOI: doi:10.1038/s41467-024-53033-7 ]
Cryo-EM Structure of MILI(K852A)-piRNA-target (26-nt)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9ij4
Q-score: 0.474
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ DOI: doi:10.1038/s41586-024-08438-1 Pubmed: 39814893 ]
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Rna (25-mer) (8 kDa, RNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Mili(k852a)-pirna-target (26-nt) (Complex from Homo sapiens)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
Cryo-EM Structure of EfPiwi-piRNA-target (25-nt, bilobed)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9iiy
Q-score: 0.315
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ DOI: doi:10.1038/s41586-024-08438-1 Pubmed: 39814893 ]
- Rna (5'-r(p*cp*gp*up*cp*up*ap*up*ap*cp*ap*ap*cp*cp*gp*ap*up*cp*ap*gp*cp*u)-3') (6 kDa, RNA from Homo sapiens)
- Efpiwi-pirna-target (25-nt, bilobed) (Complex from Homo sapiens)
- Piwi (110 kDa, Protein from Ephydatia fluviatilis)
- Rna (5'-r(p*up*ap*gp*cp*ap*gp*ap*up*cp*gp*gp*up*up*gp*up*ap*up*ap*gp*ap*cp*g)-3') (7 kDa, RNA from Homo sapiens)
Cryo-EM Structure of EfPiwi-piRNA-target (25-nt, comma)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 9iiz
Q-score: 0.214
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ DOI: doi:10.1038/s41586-024-08438-1 Pubmed: 39814893 ]
- Rna (5'-r(p*ap*gp*cp*cp*ap*ap*gp*up*up*up*cp*cp*ap*up*gp*up*up*gp*ap*up*gp*gp*up*a)-3') (7 kDa, RNA from Homo sapiens)
- Rna (25-mer) (7 kDa, RNA from Homo sapiens)
- Piwi (110 kDa, Protein from Ephydatia fluviatilis)
- Efpiwi-pirna-target (25-nt, comma) (Complex from Homo sapiens)
Cryo-EM Structure of MILI-piRNA-target (8-nt)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9ij0
Q-score: 0.417
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ DOI: doi:10.1038/s41586-024-08438-1 Pubmed: 39814893 ]
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Rna (5'-r(p*gp*ap*up*gp*gp*up*ap*a)-3') (2 kDa, RNA from Homo sapiens)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- Mili-pirna-target (8-nt) (Complex from Homo sapiens)
Cryo-EM Structure of MILI-piRNA-target (22-nt, bilobed)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9ij1
Q-score: 0.325
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ DOI: doi:10.1038/s41586-024-08438-1 Pubmed: 39814893 ]
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- Mili-pirna-target (22-nt, bilobed) (Complex from Homo sapiens)
- Rna (5'-r(p*cp*ap*ap*gp*up*up*up*cp*cp*ap*up*gp*up*up*gp*ap*up*gp*gp*up*a)-3') (6 kDa, RNA from Homo sapiens)