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) [ DOI: doi:10.1038/s41594-024-01470-9 Pubmed: 39824976 ]
- Cholesterol (386 Da, Ligand)
- Cholesterol-bound lychos (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- [(2r)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate (720 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Lysosomal cholesterol signaling protein (93 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron EG.5.1 RBD in complex with human ACE2 (local refined from the spike protein)
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8xn2
Q-score: 0.355
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
Structure (2024) 32 pp. 1055-1067.e6 [ Pubmed: 39013463 DOI: doi:10.1016/j.str.2024.06.012 ]
- Sars-cov-2 omicron eg.5.1 rbd (receptor binding domain) in complex with human ace2 (angiotensin converting enzyme 2) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s1 (25 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
SARS-CoV-2 Omicron HV.1 RBD in complex with human ACE2 (local refinement from the spike protein)
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8xn3
Q-score: 0.355
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
Structure (2024) 32 pp. 1055-1067.e6 [ Pubmed: 39013463 DOI: doi:10.1016/j.str.2024.06.012 ]
- Sars-cov-2 omicron hv.1 rbd (receptor binding domain) in complex with human ace2 (angiotensin converting enzyme 2) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Spike protein s1 (25 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of SARS-CoV-2 Omicron EG.5.1 spike protein(6P) in complex with human ACE2
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8xn5
Q-score: 0.371
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
Structure (2024) 32 pp. 1055-1067.e6 [ DOI: doi:10.1016/j.str.2024.06.012 Pubmed: 39013463 ]
- Zinc ion (65 Da, Ligand)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron eg.5.1 spike protein(6p) in complex with human ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P) in complex with human ACE2
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8xnf
Q-score: 0.317
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
Structure (2024) 32 pp. 1055-1067.e6 [ Pubmed: 39013463 DOI: doi:10.1016/j.str.2024.06.012 ]
- Sars-cov-2 omicron ba.2.86.1 spike protein(6p) in complex with human ace2 (angiotensin converting enzyme 2) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (131 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of SARS-CoV-2 Omicron HV.1 spike protein(6P) in complex with human ACE2
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8xnk
Q-score: 0.365
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
Structure (2024) 32 pp. 1055-1067.e6 [ Pubmed: 39013463 DOI: doi:10.1016/j.str.2024.06.012 ]
- Sars-cov-2 omicron hv.1 spike protein(6p) in complex with human ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of SARS-CoV-2 Omicron JN.1 spike protein in complex with human ACE2
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8y16
Q-score: 0.246
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
Structure (2024) 32 pp. 1055-1067.e6 [ Pubmed: 39013463 DOI: doi:10.1016/j.str.2024.06.012 ]
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 omicron jn.1 spike protein in complex with human ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8y18
Q-score: 0.362
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
Structure (2024) 32 pp. 1055-1067.e6 [ Pubmed: 39013463 DOI: doi:10.1016/j.str.2024.06.012 ]
- Sars-cov-2 omicron jn.1 in complex with human ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex with human ACE2 and S309 Fab
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 8y6a
Q-score: 0.343
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
Structure (2024) 32 pp. 1055-1067.e6 [ Pubmed: 39013463 DOI: doi:10.1016/j.str.2024.06.012 ]
- Heavy chain of s309 fab (24 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Spike protein s1 (26 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain of s309 fab (23 kDa, Protein from Homo sapiens)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 omicron ba.2.86 rbd in complex with human ace2 and s309 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8ww2
Q-score: 0.577
Xiong Y, Xu Z, Li X, Wang Y, Zhao J, Wang N, Duan Y, Xia R, Han Z, Qian Y, Liang J, Zhang A, Guo C, Inoue A, Xia Y, Chen Z, He Y
Cell Res (2024) 34 pp. 232-244 [ DOI: doi:10.1038/s41422-024-00932-5 Pubmed: 38287117 ]
- Gpcr/g-protein complex (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (44 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Nb35 (15 kDa, Protein from Lama glama)
- Palmitic acid (256 Da, Ligand)
- G-protein coupled receptor 3 (35 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
- Oleic acid (282 Da, Ligand)