Cryo-EM structure of the apo yeast Ceramide Synthase
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8qtn
Q-score: 0.513
Schafer JH, Clausmeyer L, Korner C, Esch BM, Wolf VN, Sapia J, Ahmed Y, Walter S, Vanni S, Januliene D, Moeller A, Frohlich F
Nat Struct Mol Biol (2024) [ Pubmed: 39528796 DOI: doi:10.1038/s41594-024-01415-2 ]
- Ceramide synthase subunit lip1 (15 kDa, Protein from Saccharomyces cerevisiae)
- Ceramide synthase lag1 (37 kDa, Protein from Saccharomyces cerevisiae)
- [(2s)-1-hexadecanoyloxy-3-[hydroxy-[(2s,3r,5s,6r)-2,3,4,5,6-pentahydroxycyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] heptadecanoate (825 Da, Ligand)
- Ceramide synthase lac1 (36 kDa, Protein from Saccharomyces cerevisiae)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Ammonium ion (18 Da, Ligand)
- Hexacosanoic acid (396 Da, Ligand)
- Heterotetrameric complex of yeast ceramide synthase with lag1, lac1 and lip1 (140 kDa, Complex from Saccharomyces cerevisiae)
Cryo-EM structure of the FB-bound yeast Ceramide Synthase
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8qtr
Q-score: 0.464
Schafer JH, Clausmeyer L, Korner C, Esch BM, Wolf VN, Sapia J, Ahmed Y, Walter S, Vanni S, Januliene D, Moeller A, Frohlich F
Nat Struct Mol Biol (2024) [ Pubmed: 39528796 DOI: doi:10.1038/s41594-024-01415-2 ]
- Ceramide synthase lac1 (35 kDa, Protein from Saccharomyces cerevisiae)
- Macrofusine (721 Da, Ligand)
- Ceramide synthase lag1 (37 kDa, Protein from Saccharomyces cerevisiae)
- [(2s)-1-hexadecanoyloxy-3-[hydroxy-[(2s,3r,5s,6r)-2,3,4,5,6-pentahydroxycyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] heptadecanoate (825 Da, Ligand)
- Ammonium ion (18 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Ceramide synthase subunit lip1 (15 kDa, Protein from Saccharomyces cerevisiae)
- Hexacosanoic acid (396 Da, Ligand)
- Heterotetrameric complex of yeast ceramide synthase with lag1, lac1 and lip1 (140 kDa, Complex from Saccharomyces cerevisiae)
CryoEM structure of human rho1 GABAA receptor apo state
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 8oq6
Q-score: 0.559
Cowgill J, Fan C, Haloi N, Tobiasson V, Zhuang Y, Howard RJ, Lindahl E
Neuron (2023) 111 pp. 3450- [ DOI: doi:10.1016/j.neuron.2023.08.006 Pubmed: 37659407 ]
- Water (18 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit rho-1 (55 kDa, Protein from Homo sapiens)
- Human rho1 gabaa receptor (Complex from Homo sapiens)
- N-octane (114 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- [(2r)-2-heptanoyloxy-3-phosphonooxy-propyl] nonanoate (424 Da, Ligand)
- Decane (142 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
CryoEM structure of human rho1 GABAA receptor in complex with pore blocker picrotoxin
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8oq8
Q-score: 0.628
Cowgill J, Fan C, Haloi N, Tobiasson V, Zhuang Y, Howard RJ, Lindahl E
Neuron (2023) 111 pp. 3450- [ DOI: doi:10.1016/j.neuron.2023.08.006 Pubmed: 37659407 ]
- Rho1 gabaa receptor (Complex from Homo sapiens)
- Hexane (86 Da, Ligand)
- Water (18 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit rho-1 (55 kDa, Protein from Homo sapiens)
- Dodecane (170 Da, Ligand)
- Decane (142 Da, Ligand)
- (1ar,2ar,3s,6r,6as,8as,8br,9r)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3h)-dione (292 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
CryoEM structure of human rho1 GABAA receptor in complex with GABA and picrotoxin
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8oqa
Q-score: 0.604
Cowgill J, Fan C, Haloi N, Tobiasson V, Zhuang Y, Howard RJ, Lindahl E
Neuron (2023) 111 pp. 3450-3464.e5 [ DOI: doi:10.1016/j.neuron.2023.08.006 Pubmed: 37659407 ]
- Hexane (86 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit rho-1 (55 kDa, Protein from Homo sapiens)
- Human rho1 gabaa receptor (Complex from Homo sapiens)
- N-octane (114 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- (1ar,2ar,3s,6r,6as,8as,8br,9r)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3h)-dione (292 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
PSII-Pcb Dimer of Acaryochloris Marina
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7ymi
Q-score: 0.538
Shen L, Gao Y, Tang K, Qi R, Fu L, Chen JH, Wang W, Ma X, Li P, Chen M, Kuang T, Zhang X, Shen JR, Wang P, Han G
Sci Adv (2024) 10 pp. eadk7140-eadk7140 [ DOI: doi:10.1126/sciadv.adk7140 Pubmed: 38394197 ]
- Photosystem ii protein psbi (3 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center x protein (4 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (37 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii protein d1 2 (39 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein ycf12 (4 kDa, Protein from Acaryochloris marina MBIC11017)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Unknown protein (3 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein t (5 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii protein y (11 kDa, Protein from Acaryochloris marina MBIC11017)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii d2 protein 1 (39 kDa, Protein from Acaryochloris marina MBIC11017)
- Psii-pcb dimer of acaryochloris marina (Complex from Acaryochloris marina MBIC11017)
- Chlorophyll d (895 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Acaryochloris marina MBIC11017)
- Fe (ii) ion (55 Da, Ligand)
- (1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
- Photosystem ii 10 kda phosphoprotein psbh (7 kDa, Protein from Acaryochloris marina MBIC11017)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii cp43 reaction center protein (53 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Acaryochloris marina MBIC11017)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
PSII-Pcb Tetramer of Acaryochloris Marina
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7ymm
Q-score: 0.415
Shen L, Gao Y, Tang K, Qi R, Fu L, Chen JH, Wang W, Ma X, Li P, Chen M, Kuang T, Zhang X, Shen JR, Wang P, Han G
Sci Adv (2024) 10 pp. eadk7140-eadk7140 [ DOI: doi:10.1126/sciadv.adk7140 Pubmed: 38394197 ]
- Photosystem ii protein psbi (3 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center x protein (4 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Psii-pcb tetramer of acaryochloris marina (Complex from Acaryochloris marina MBIC11017)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (37 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii protein d1 2 (39 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein ycf12 (4 kDa, Protein from Acaryochloris marina MBIC11017)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Unknown protein (3 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein t (5 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii protein y (11 kDa, Protein from Acaryochloris marina MBIC11017)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii d2 protein 1 (39 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Acaryochloris marina MBIC11017)
- Chlorophyll d (895 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Acaryochloris marina MBIC11017)
- Fe (ii) ion (55 Da, Ligand)
- (1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
- Photosystem ii 10 kda phosphoprotein psbh (7 kDa, Protein from Acaryochloris marina MBIC11017)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii cp43 reaction center protein (53 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Acaryochloris marina MBIC11017)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
momSalB bound Kappa Opioid Receptor in complex with Gi1
Resolution: 2.71 Å
EM Method: Single-particle
Fitted PDBs: 8dzp
Q-score: 0.533
Han J, Zhang J, Nazarova AL, Bernhard SM, Krumm BE, Zhao L, Lam JH, Rangari VA, Majumdar S, Nichols DE, Katritch V, Yuan P, Fay JF, Che T
Nature (2023) 617 pp. 417-425 [ DOI: doi:10.1038/s41586-023-06030-7 Pubmed: 37138078 ]
- Momsalb bound kappa opioid receptor in complex with gi1 (Complex from Homo sapiens)
- Methyl (2s,4ar,6ar,7r,9s,10as,10br)-2-(furan-3-yl)-9-(methoxymethoxy)-6a,10b-dimethyl-4,10-dioxododecahydro-2h-naphtho[2,1-c]pyran-7-carboxylate (434 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(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Scfv16 protein (26 kDa, Protein from Mus musculus)
- Kappa-type opioid receptor (34 kDa, Protein from Homo sapiens)
momSalB bound Kappa Opioid Receptor in complex with GoA
Resolution: 2.82 Å
EM Method: Single-particle
Fitted PDBs: 8dzq
Q-score: 0.459
Han J, Zhang J, Nazarova AL, Bernhard SM, Krumm BE, Zhao L, Lam JH, Rangari VA, Majumdar S, Nichols DE, Katritch V, Yuan P, Fay JF, Che T
Nature (2023) 617 pp. 417-425 [ DOI: doi:10.1038/s41586-023-06030-7 Pubmed: 37138078 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Methyl (2s,4ar,6ar,7r,9s,10as,10br)-2-(furan-3-yl)-9-(methoxymethoxy)-6a,10b-dimethyl-4,10-dioxododecahydro-2h-naphtho[2,1-c]pyran-7-carboxylate (434 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Momsalb bound kappa opioid receptor in complex with goa (Complex from Homo sapiens)
- Scfv16 protein (26 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(o) subunit alpha (40 kDa, Protein from Homo sapiens)
- Kappa-type opioid receptor (34 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human cholesterol transporter ABCG1 in complex with cholesterol
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 7fdv
Q-score: 0.528
Xu D, Li Y, Yang F, Sun CR, Pan J, Wang L, Chen ZP, Fang SC, Yao X, Hou WT, Zhou CZ, Chen Y
Cell Rep (2022) 38 pp. 110298-110298 [ DOI: doi:10.1016/j.celrep.2022.110298 Pubmed: 35081353 ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- The complex of human abcg1 with cholesterol and atp (152 kDa, Complex from Homo sapiens)
- Atp-binding cassette sub-family g member 1 (75 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- [(e,2s,3r)-2-(hexadecanoylamino)-3-oxidanyl-octadec-4-enyl] 2-(trimethylazaniumyl)ethyl phosphate (703 Da, Ligand)