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)
Curved structure of mPIEZO1-S2472E
Resolution: 4.07 Å
EM Method: Single-particle
Fitted PDBs: 8ixn
Q-score: 0.301
Liu S, Yang X, Chen X, Zhang X, Jiang J, Yuan J, Liu W, Wang L, Zhou H, Wu K, Tian B, Li X, Xiao B
Neuron (2024) [ Pubmed: 39719701 DOI: doi:10.1016/j.neuron.2024.11.020 ]
- Piezo-type mechanosensitive ion channel component 1 (292 kDa, Protein from Mus musculus)
- (9r,11s)-9-({[(1s)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2lambda~5~-aza-6lambda~5~-phosphaoctacosane-6,6,11-triol (767 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- S2472e-curved structure (Complex from Mus musculus)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
Flattened structure of mPIEZO1-S2472E
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8ixo
Q-score: 0.445
Liu S, Yang X, Chen X, Zhang X, Jiang J, Yuan J, Liu W, Wang L, Zhou H, Wu K, Tian B, Li X, Xiao B
Neuron (2024) [ Pubmed: 39719701 DOI: doi:10.1016/j.neuron.2024.11.020 ]
- Piezo-type mechanosensitive ion channel component 1 (292 kDa, Protein from Mus musculus)
- S2472e-intermediate structure (Complex from Mus musculus)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- (9r,11s)-9-({[(1s)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2lambda~5~-aza-6lambda~5~-phosphaoctacosane-6,6,11-triol (767 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
Resolution: 2.11 Å
EM Method: Single-particle
Fitted PDBs: 8z8z
Q-score: 0.589
Xiong Q, Zhu Z, Li T, Li X, Zhou Z, Chao Y, Yang C, Feng S, Qu Q, Li D
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01474-5 Pubmed: 39824977 ]
- Water (18 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (4~{z},7~{z},10~{z},13~{z},16~{z},19~{z})-docosa-4,7,10,13,16,19-hexaenoate (764 Da, Ligand)
- Lychos (127 kDa, Complex from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Lysosomal cholesterol signaling protein,fluorescent protein (127 kDa, Protein from synthetic construct)
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) [ DOI: doi:10.1111/jipb.13816 Pubmed: 39670505 ]
- Tp-lhcr20 (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c light-harvesting protein (19 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)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c light-harvesting protein (23 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit xi (15 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)
- Fucoxanthin chl a/c light-harvesting protein (19 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein, major type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit psa29 (13 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Tp-lhcr18 (16 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)
- 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)
- Pt17531-like protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Chlorophyll c1 (610 Da, Ligand)
- Fucoxanthin chl a/c light-harvesting protein, lhcr type (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Fucoxanthin chl a/c light-harvesting protein (18 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Chlorophyll a (893 Da, Ligand)
- Tp-redcap (20 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Photosystem i reaction center subunit iii (17 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 p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Tp-psar (9 kDa, Protein from Thalassiosira pseudonana CCMP1335)
- Beta-carotene (536 Da, Ligand)
- Tp-psi-fcpi-l (Complex from Thalassiosira pseudonana CCMP1335)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit viii (3 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 ]
- Pwadh-g88d-d344n (Complex from Pseudoxanthomonas wuyuanensis)
- (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)
- Zinc ion (65 Da, Ligand)
- Imidazolonepropionase (43 kDa, Protein from Pseudoxanthomonas wuyuanensis)
Cryo-EM structure of NRG1A(LRR) in complex with EDS1-SAG101-(ADPr-ATP)
Huang S, Wang J, Song R, Jia A, Xiao Y, Sun Y, Wang L, Mahr D, Wu Z, Han Z, Li X, Parker JE, Chai J
Nature (2025) [ DOI: doi:10.1038/s41586-024-08521-7 ]
- Probable disease resistance protein at5g66900 (46 kDa, Protein from Arabidopsis thaliana)
- Adenosine-5-diphosphoribose (559 Da, Ligand)
- Protein eds1 (70 kDa, Protein from Arabidopsis thaliana)
- Ternary complex of nrg1a(lrr) with eds1-sag101-(adpr-atp) (Complex from Arabidopsis)
- Senescence-associated carboxylesterase 101 (61 kDa, Protein from Arabidopsis thaliana)
- Adenosine-5'-triphosphate (507 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 [ DOI: doi:10.1038/s41467-024-52585-y Pubmed: 39333117 ]
- 4-(1h-imidazol-4-ylmethyl)pyridine (159 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Engineered guanine nucleotide-binding protein g(o) subunit alpha,guanine nucleotide-binding protein g(o) subunit alpha (25 kDa, Protein from synthetic construct)
- Antibody fragment scfv16 (27 kDa, Protein from synthetic construct)
- Immethridine-h3r-minigo-scfv16 complex (Complex from Homo sapiens)
- 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-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 [ DOI: doi:10.1038/s41467-024-52585-y Pubmed: 39333117 ]
- Cholesterol (386 Da, Ligand)
- Histamine h3 receptor (72 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Homo sapiens)
- Proxyfan-h3r-minigo-scfv16 complex (Complex from Homo sapiens)
- Antibody fragment scfv16 (27 kDa, Protein from synthetic construct)
- 5-(3-phenylmethoxypropyl)-1h-imidazole (216 Da, Ligand)
- Engineered guanine nucleotide-binding protein g(o) subunit alpha,guanine nucleotide-binding protein g(o) subunit alpha (25 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 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 ]
- Imidazolonepropionase (43 kDa, Protein from Pseudoxanthomonas wuyuanensis)
- Pwadh (Complex from Pseudoxanthomonas wuyuanensis)
- Zinc ion (65 Da, Ligand)