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)
PSI-FCPI-L in Thalassiosira pseudonana
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8zeh
Q-score: 0.566
Feng Y, Li Z, Yang Y, Shen L, Li X, Liu X, Zhang X, Zhang J, Ren F, Wang Y, Liu C, Han G, Wang X, Kuang T, Shen JR, Wang W
J Integr Plant Biol (2024) [ Pubmed: 39670505 DOI: doi:10.1111/jipb.13816 ]
- Fucoxanthin chl a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Beta-carotene (536 Da, Ligand)
- Fucoxanthin chlorophyll a/c light-harvesting protein (23 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (1~{r})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-lhcr20 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Tp-lhcr18 (16 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-psi-fcpi-l (Complex from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Phylloquinone (450 Da, Ligand)
- Fucoxanthin chl a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll c1 (610 Da, Ligand)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Tp-PSI-FCPI-S in Thalassiosira pseudonana
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8zet
Q-score: 0.485
Feng Y, Li Z, Yang Y, Shen L, Li X, Liu X, Zhang X, Zhang J, Ren F, Wang Y, Liu C, Han G, Wang X, Kuang T, Shen JR, Wang W
J Integr Plant Biol (2024) [ Pubmed: 39670505 DOI: doi:10.1111/jipb.13816 ]
- Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (1~{r})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e})-3,7,12,16-tetramethyl-18-[(4~{r})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol (566 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Phylloquinone (450 Da, Ligand)
- Tp-psi-fcpi-s (Complex from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Iron/sulfur cluster (351 Da, Ligand)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Chlorophyll c1 (610 Da, Ligand)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thalassiosira pseudonana CCMP1335)
Resolution: 2.37 Å
EM Method: Single-particle
Fitted PDBs: 8yak
Q-score: 0.652
Hu Y, Dai L, Xu Y, Niu D, Yang X, Xie Z, Shen P, Li X, Li H, Zhang L, Min J, Guo RT, Chen CC
Int J Biol Macromol (2024) 278 pp. 134831-134831 [ Pubmed: 39163957 DOI: doi:10.1016/j.ijbiomac.2024.134831 ]
- (2~{s})-2-[[(3~{r})-5-chloranyl-3-methyl-8-oxidanyl-1-oxidanylidene-3,4-dihydroisochromen-7-yl]carbonylamino]-3-phenyl-propanoic acid (403 Da, Ligand)
- Imidazolonepropionase (43 kDa, Protein from Pseudoxanthomonas wuyuanensis)
- Pwadh-g88d-d344n (Complex from Pseudoxanthomonas wuyuanensis)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of histamine H3 receptor in complex with immethridine and miniGo
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8yn7
Q-score: 0.548
Zhang X, Liu G, Zhong YN, Zhang R, Yang CC, Niu C, Pu X, Sun J, Zhang T, Yang L, Zhang C, Li X, Shen X, Xiao P, Sun JP, Gong W
Nat Commun (2024) 15 pp. 8296-8296 [ Pubmed: 39333117 DOI: doi:10.1038/s41467-024-52585-y ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Antibody fragment scfv16 (27 kDa, Protein from synthetic construct)
- 4-(1h-imidazol-4-ylmethyl)pyridine (159 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Engineered guanine nucleotide-binding protein g(o) subunit alpha,guanine nucleotide-binding protein g(o) subunit alpha (25 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Homo sapiens)
- Histamine h3 receptor (72 kDa, Protein from Homo sapiens)
- Immethridine-h3r-minigo-scfv16 complex (Complex from Homo sapiens)
Cryo-EM structure of histamine H3 receptor in complex with proxyfan and miniGo
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8yn8
Q-score: 0.544
Zhang X, Liu G, Zhong YN, Zhang R, Yang CC, Niu C, Pu X, Sun J, Zhang T, Yang L, Zhang C, Li X, Shen X, Xiao P, Sun JP, Gong W
Nat Commun (2024) 15 pp. 8296-8296 [ Pubmed: 39333117 DOI: doi:10.1038/s41467-024-52585-y ]
- Engineered guanine nucleotide-binding protein g(o) subunit alpha,guanine nucleotide-binding protein g(o) subunit alpha (25 kDa, Protein from Homo sapiens)
- Antibody fragment scfv16 (27 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Proxyfan-h3r-minigo-scfv16 complex (Complex from Homo sapiens)
- 5-(3-phenylmethoxypropyl)-1h-imidazole (216 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Homo sapiens)
- Histamine h3 receptor (72 kDa, Protein from Homo sapiens)
Cryo-electron microscopic structure of an amide hydrolase from Pseudoxanthomonas wuyuanensis
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 8yag
Q-score: 0.665
Hu Y, Dai L, Xu Y, Niu D, Yang X, Xie Z, Shen P, Li X, Li H, Zhang L, Min J, Guo RT, Chen CC
Int J Biol Macromol (2024) 278 pp. 134831-134831 [ Pubmed: 39163957 DOI: doi:10.1016/j.ijbiomac.2024.134831 ]
- Pwadh (Complex from Pseudoxanthomonas wuyuanensis)
- Imidazolonepropionase (43 kDa, Protein from Pseudoxanthomonas wuyuanensis)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of histamine H1 receptor in complex with histamine and miniGq
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8yn2
Q-score: 0.578
Zhang X, Liu G, Zhong YN, Zhang R, Yang CC, Niu C, Pu X, Sun J, Zhang T, Yang L, Zhang C, Li X, Shen X, Xiao P, Sun JP, Gong W
Nat Commun (2024) 15 pp. 8296-8296 [ Pubmed: 39333117 DOI: doi:10.1038/s41467-024-52585-y ]
- Antibody fragment scfv16 (27 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Histamine h1 receptor (80 kDa, Protein from Homo sapiens)
- Histamine-h1r-minigq-scfv16 complex (Complex from Homo sapiens)
- Histamine (111 Da, Ligand)
- Engineered guanine nucleotide-binding protein g(q) subunit alpha (28 kDa, Protein from synthetic construct)
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Homo sapiens)
Cryo-EM structure of histamine H2 receptor in complex with histamine and miniGs
Resolution: 2.56 Å
EM Method: Single-particle
Fitted PDBs: 8yn3
Q-score: 0.623
Zhang X, Liu G, Zhong YN, Zhang R, Yang CC, Niu C, Pu X, Sun J, Zhang T, Yang L, Zhang C, Li X, Shen X, Xiao P, Sun JP, Gong W
Nat Commun (2024) 15 pp. 8296-8296 [ Pubmed: 39333117 DOI: doi:10.1038/s41467-024-52585-y ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Nanobody nb35 (15 kDa, Protein from synthetic construct)
- Histamine-h2r-minigs-nb35 complex (Complex from Homo sapiens)
- Histamine h2 receptor (62 kDa, Protein from Homo sapiens)
- Histamine (111 Da, Ligand)
- Engineered guanine nucleotide,binding protein g(s) subunit alpha (29 kDa, Protein from synthetic construct)
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Homo sapiens)
Cryo-EM structure of histamine H2 receptor in complex with histamine and miniGq
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8yn4
Q-score: 0.515
Zhang X, Liu G, Zhong YN, Zhang R, Yang CC, Niu C, Pu X, Sun J, Zhang T, Yang L, Zhang C, Li X, Shen X, Xiao P, Sun JP, Gong W
Nat Commun (2024) 15 pp. 8296-8296 [ Pubmed: 39333117 DOI: doi:10.1038/s41467-024-52585-y ]
- Histamine-h2r-minigq-scfv16 complex (Complex from Homo sapiens)
- Antibody fragment scfv16 (27 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Histamine h2 receptor (62 kDa, Protein from Homo sapiens)
- Histamine (111 Da, Ligand)
- Engineered guanine nucleotide-binding protein g(q) subunit alpha (28 kDa, Protein from synthetic construct)
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Homo sapiens)