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)
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)
Structure of chanoclavine synthase from Claviceps fusiformis
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 9jdb
Q-score: 0.633
Liu ZW, Wang T, Li X, Shen PP, Huang J-W, Chen C-C, Guo R-T
To Be Published
- Catalase easc (54 kDa, Protein from Claviceps fusiformis)
- Ergot alkaloid synthesis protein c (Complex from Claviceps fusiformis)
- Protoporphyrin ix containing fe (616 Da, Ligand)
Structure of chanoclavine synthase from Claviceps fusiformis in complex with prechanoclavine
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 9jdc
Q-score: 0.693
Liu ZW, Wang T, Li X, Shen PP, Huang J-W, Chen C-C, Guo R-T
To Be Published
- Catalase easc (54 kDa, Protein from Claviceps fusiformis)
- Ergot alkaloid synthesis protein c (Complex from Claviceps fusiformis)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (2~{s})-2-(methylamino)-3-[4-[(1~{e})-3-methylbuta-1,3-dienyl]-1~{h}-indol-3-yl]propanoic acid (284 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 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)
Cryo-EM Structure of MILI-piRNA-target (26-nt)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9ij3
Q-score: 0.463
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)
- Mili-pirna-target (26-nt) (Complex from Homo sapiens)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
- Manganese (ii) ion (54 Da, Ligand)