Gisriel CJ, Kurashov V, Iwig DF, Russell BP, Vinyard DJ, Brudvig GW, Golbeck JH, Lakshmi KV
Sci Adv (2024) 10 pp. eadp4937-eadp4937 [ DOI: doi:10.1126/sciadv.adp4937 Pubmed: 39612342 ]
- Menb photosystem i (Complex from Synechocystis sp. PCC 6803)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Synechocystis sp. PCC 6803)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Synechocystis sp. PCC 6803)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechocystis sp. PCC 6803)
- (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 i reaction center subunit ix (4 kDa, Protein from Synechocystis sp. PCC 6803)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Synechocystis sp. PCC 6803)
- 2,3-dimethyl-5-[(2e,7r,11r)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione (414 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Synechocystis sp. PCC 6803)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem i reaction center subunit psak 2 (9 kDa, Protein from Synechocystis sp. PCC 6803)
- Calcium ion (40 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Synechocystis sp. PCC 6803)
- (3'r)-3'-hydroxy-beta,beta-caroten-4-one (566 Da, Ligand)
- Beta,beta-carotene-4,4'-dione (564 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechocystis sp. PCC 6803)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit iii (18 kDa, Protein from Synechocystis sp. PCC 6803)
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 ]
- Heterotetrameric complex of yeast ceramide synthase with lag1, lac1 and lip1 (140 kDa, Complex from Saccharomyces cerevisiae)
- Ammonium ion (18 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Hexacosanoic acid (396 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)
- Ceramide synthase subunit lip1 (15 kDa, Protein from Saccharomyces cerevisiae)
- Ceramide synthase lac1 (36 kDa, Protein 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 ]
- Heterotetrameric complex of yeast ceramide synthase with lag1, lac1 and lip1 (140 kDa, Complex from Saccharomyces cerevisiae)
- Ceramide synthase lac1 (35 kDa, Protein from Saccharomyces cerevisiae)
- Ceramide synthase subunit lip1 (15 kDa, Protein from Saccharomyces cerevisiae)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Ammonium ion (18 Da, Ligand)
- Macrofusine (721 Da, Ligand)
- Hexacosanoic acid (396 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)
Cryo-EM structure of Dopamine 3 Receptor:Go complex bound to bitopic FOB02-04A - Conformation A
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 9f33
Q-score: 0.528
Arroyo-Urea S, Nazarova AL, Carrion-Antoli A, Bonifazi A, Battiti FO, Lam JH, Newman AH, Katritch V, Garcia-Nafria J
Nat Commun (2024) 15 pp. 7759-7759 [ DOI: doi:10.1038/s41467-024-51993-4 Pubmed: 39237617 ]
- Guanine nucleotide-binding protein g(o) subunit alpha (40 kDa, Protein from Homo sapiens)
- Green fluorescent protein,d(3) dopamine receptor (74 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- N-[2-[(1r,2s)-2-[[(2s,5s)-2-(6-azanylpyridin-3-yl)-5-methyl-morpholin-4-yl]methyl]cyclopropyl]ethyl]-1h-indole-2-carboxamide (433 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Rattus norvegicus)
- D3r:go protein complex with bitopic fob02-04a-conformation a (190 kDa, Complex from Homo sapiens)
- Antibody scfv16 (28 kDa, Protein from Mus musculus)
Cryo-EM structure of Dopamine 3 receptor:Go complex bound to bitopic FOB02-04A - Conformation B
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 9f34
Q-score: 0.456
Arroyo-Urea S, Nazarova AL, Carrion-Antoli A, Bonifazi A, Battiti FO, Lam JH, Newman AH, Katritch V, Garcia-Nafria J
Nat Commun (2024) 15 pp. 7759-7759 [ DOI: doi:10.1038/s41467-024-51993-4 Pubmed: 39237617 ]
- Guanine nucleotide-binding protein g(o) subunit alpha (40 kDa, Protein from Homo sapiens)
- Green fluorescent protein,d(3) dopamine receptor (74 kDa, Protein from Homo sapiens)
- Antibody scfv16 (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- N-[2-[(1r,2s)-2-[[(2s,5s)-2-(6-azanylpyridin-3-yl)-5-methyl-morpholin-4-yl]methyl]cyclopropyl]ethyl]-1h-indole-2-carboxamide (433 Da, Ligand)
- D3r: gtrimer: scfv16 complex bound to the bitopic fob02-04a - conformation b (190 kDa, Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Rattus norvegicus)
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 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit rho-1 (55 kDa, Protein from Homo sapiens)
- Human rho1 gabaa receptor (Complex from Homo sapiens)
- [(2r)-2-heptanoyloxy-3-phosphonooxy-propyl] nonanoate (424 Da, Ligand)
- Decane (142 Da, Ligand)
- N-octane (114 Da, Ligand)
- Water (18 Da, Ligand)
- Chloride ion (35 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 ]
- Hexane (86 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Rho1 gabaa receptor (Complex from Homo sapiens)
- (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)
- Gamma-aminobutyric acid receptor subunit rho-1 (55 kDa, Protein from Homo sapiens)
- Decane (142 Da, Ligand)
- Water (18 Da, Ligand)
- Dodecane (170 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)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 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)
- 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)
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 [ Pubmed: 38394197 DOI: doi:10.1126/sciadv.adk7140 ]
- Photosystem ii protein d1 2 (39 kDa, Protein from Acaryochloris marina MBIC11017)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll d (895 Da, Ligand)
- Photosystem ii reaction center protein k (4 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)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Acaryochloris marina MBIC11017)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Acaryochloris marina MBIC11017)
- Psii-pcb dimer of acaryochloris marina (Complex from Acaryochloris marina MBIC11017)
- (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)
- Unknown protein (3 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii protein y (11 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii cp43 reaction center protein (53 kDa, Protein from Acaryochloris marina MBIC11017)
- Pheophytin a (871 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii reaction center x protein (4 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii 10 kda phosphoprotein psbh (7 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein t (5 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii protein psbi (3 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein m (3 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii d2 protein 1 (39 kDa, Protein from Acaryochloris marina MBIC11017)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- High light inducible protein (37 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein l (4 kDa, Protein from Acaryochloris marina MBIC11017)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 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)
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 [ Pubmed: 38394197 DOI: doi:10.1126/sciadv.adk7140 ]
- Photosystem ii protein d1 2 (39 kDa, Protein from Acaryochloris marina MBIC11017)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll d (895 Da, Ligand)
- Photosystem ii reaction center protein k (4 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 (Complex from Acaryochloris marina MBIC11017)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Acaryochloris marina MBIC11017)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Acaryochloris marina MBIC11017)
- (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)
- Unknown protein (3 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- High light inducible protein (38 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii protein y (11 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii cp43 reaction center protein (53 kDa, Protein from Acaryochloris marina MBIC11017)
- Pheophytin a (871 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii reaction center x protein (4 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii 10 kda phosphoprotein psbh (7 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein t (5 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii protein psbi (3 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein m (3 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii d2 protein 1 (39 kDa, Protein from Acaryochloris marina MBIC11017)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- High light inducible protein (37 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem ii reaction center protein l (4 kDa, Protein from Acaryochloris marina MBIC11017)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 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)