CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with GABA and puerarin
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 9eqg
Q-score: 0.627
Lyu Q, Xue W, Liu R, Ma Q, Kasaragod VB, Sun S, Li Q, Chen Y, Yuan M, Yang Y, Zhang B, Nie A, Jia S, Shen C, Gao P, Rong W, Yu C, Bi Y, Zhang C, Nan F, Ning G, Rao Z, Yang X, Wang J, Wang W
Nature (2024) 634 pp. 936-943 [ Pubmed: 39261733 DOI: doi:10.1038/s41586-024-07929-5 ]
- Hexadecane (226 Da, Ligand)
- 1,2-dilauroyl-sn-glycero-3-phosphate (535 Da, Ligand)
- Hexane (86 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit gamma-2 (56 kDa, Protein from Homo sapiens)
- Gamma-aminobutyric acid receptor subunit alpha-1 (52 kDa, Protein from Homo sapiens)
- Palmitic acid (256 Da, Ligand)
- Water (18 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Cryoem structure of human full-length alpha1beta3gamma2l gaba(a)r in complex with gaba and puerarin (250 kDa, Complex from Homo sapiens)
- Chloride ion (35 Da, Ligand)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Decane (142 Da, Ligand)
- [(2r)-1-octadecanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8z)-icosa-5,8,11,14-tetraenoate (1 kDa, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Puerarin (416 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8ovc
Q-score: 0.598
Riepl D, Gamiz-Hernandez AP, Kovalova T, Krol SM, Mader SL, Sjostrand D, Hogbom M, Brzezinski P, Kaila VRI
Nat Commun (2024) 15 pp. 5276-5276 [ Pubmed: 38902248 DOI: doi:10.1038/s41467-024-49628-9 ]
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Co-purified unknown peptide (869 Da, Protein from Mycolicibacterium smegmatis)
- Calcium ion (40 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Heme c (618 Da, Ligand)
- Water (18 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- Co-purified unknown peptide (2 kDa, Protein from Mycolicibacterium smegmatis)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
ST171-bound serotonin 5-HT1A receptor - Gi Protein Complex
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8pjk
Q-score: 0.611
Ullrich A, Schneider J, Braz JM, Neu E, Staffen N, Stanek M, Blahova J, Hove T, Albert T, Allikalt A, Lober S, Bhardwaj K, Rodriguez-Rosado S, Fink E, Rasmussen T, Hubner H, Inoue A, Shoichet BK, Basbaum AJ, Bottcher B, Weikert D, Gmeiner P
bioRxiv (2023) [ DOI: doi:10.1101/2023.09.11.557127 ]
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- St171-bound serotonin 5-ht1a receptor - gi protein complex (Complex from Homo sapiens)
- (2r)-1-(heptadecanoyloxy)-3-{[(r)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5z,8z,11z,14z)-icosa-5,8,11,14-tetraenoate (953 Da, Ligand)
- 6-[3-[2-(2-methoxyphenoxy)ethylamino]propoxy]-4~{h}-1,4-benzoxazin-3-one (372 Da, Ligand)
- 5-hydroxytryptamine receptor 1a (51 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
Befiradol-bound serotonin 5-HT1A receptor - Gi Protein Complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8pkm
Q-score: 0.468
Ullrich A, Schneider J, Braz JM, Neu E, Staffen N, Stanek M, Blahova J, Hove T, Albert T, Allikalt A, Lober S, Bhardwaj K, Rodriguez-Rosado S, Fink E, Rasmussen T, Hubner H, Inoue A, Shoichet BK, Basbaum AJ, Bottcher B, Weikert D, Gmeiner P
bioRxiv (2023) [ DOI: doi:10.1101/2023.09.11.557127 ]
- 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)
- (2r)-1-(heptadecanoyloxy)-3-{[(r)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5z,8z,11z,14z)-icosa-5,8,11,14-tetraenoate (953 Da, Ligand)
- (3-chloranyl-4-fluoranyl-phenyl)-[4-fluoranyl-4-[[(5-methylpyridin-2-yl)methylamino]methyl]piperidin-1-yl]methanone (393 Da, Ligand)
- 5-hydroxytryptamine receptor 1a (51 kDa, Protein from Homo sapiens)
- Befiradol-bound serotonin 5-ht1a receptor - gi protein complex (Complex from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (38 kDa, Protein from Homo sapiens)
5-MeO-DMT-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8fy8
Q-score: 0.519
Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D
Nature (2024) 630 pp. 237-246 [ DOI: doi:10.1038/s41586-024-07403-2 Pubmed: 38720072 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- 2-(5-methoxy-1h-indol-3-yl)-n,n-dimethylethan-1-amine (218 Da, Ligand)
- Serotonin 1a (5-ht1a) receptor-gi1 protein complex (Complex from Escherichia coli, Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (8 kDa, Protein from Homo sapiens)
- [(2r)-1-[oxidanyl-[(2r,3r,5s,6r)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5e,8e)-hexadeca-5,8,11,14-tetraenoate (854 Da, Ligand)
- Soluble cytochrome b562,5-hydroxytryptamine receptor 1a,5-hydroxytryptamine receptor 1a (61 kDa, Protein from Homo sapiens)
4-F, 5-MeO-PyrT-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8fye
Q-score: 0.53
Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D
Nature (2024) 630 pp. 237-246 [ DOI: doi:10.1038/s41586-024-07403-2 Pubmed: 38720072 ]
- 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 (39 kDa, Protein from Homo sapiens)
- Serotonin 1a (5-ht1a) receptor-gi1 protein complex (Complex from Escherichia coli, Homo sapiens)
- 4-fluoro-5-methoxy-3-[2-(pyrrolidin-1-yl)ethyl]-1h-indole (262 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (8 kDa, Protein from Homo sapiens)
- [(2r)-1-[oxidanyl-[(2r,3r,5s,6r)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5e,8e)-hexadeca-5,8,11,14-tetraenoate (854 Da, Ligand)
- Soluble cytochrome b562,5-hydroxytryptamine receptor 1a,5-hydroxytryptamine receptor 1a (61 kDa, Protein from Homo sapiens)
Vilazodone-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8fyl
Q-score: 0.525
Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D
Nature (2024) 630 pp. 237-246 [ DOI: doi:10.1038/s41586-024-07403-2 Pubmed: 38720072 ]
- 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 (39 kDa, Protein from Homo sapiens)
- Serotonin 1a (5-ht1a) receptor-gi1 protein complex (Complex from Escherichia coli, Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (8 kDa, Protein from Homo sapiens)
- 5-{4-[4-(5-cyano-1h-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide (441 Da, Ligand)
- [(2r)-1-[oxidanyl-[(2r,3r,5s,6r)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5e,8e)-hexadeca-5,8,11,14-tetraenoate (854 Da, Ligand)
- Soluble cytochrome b562,5-hydroxytryptamine receptor 1a,5-hydroxytryptamine receptor 1a (61 kDa, Protein from Homo sapiens)
LSD-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8fyt
Q-score: 0.544
Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D
Nature (2024) 630 pp. 237-246 [ DOI: doi:10.1038/s41586-024-07403-2 Pubmed: 38720072 ]
- 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 (39 kDa, Protein from Homo sapiens)
- Serotonin 1a (5-ht1a) receptor-gi1 protein complex (Complex from Escherichia coli, Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (8 kDa, Protein from Homo sapiens)
- (8alpha)-n,n-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide (323 Da, Ligand)
- [(2r)-1-[oxidanyl-[(2r,3r,5s,6r)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5e,8e)-hexadeca-5,8,11,14-tetraenoate (854 Da, Ligand)
- Soluble cytochrome b562,5-hydroxytryptamine receptor 1a,5-hydroxytryptamine receptor 1a (61 kDa, Protein from Homo sapiens)
Buspirone-bound serotonin 1A (5-HT1A) receptor-Gi1 protein complex
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 8fyx
Q-score: 0.545
Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D
Nature (2024) 630 pp. 237-246 [ DOI: doi:10.1038/s41586-024-07403-2 Pubmed: 38720072 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Serotonin 1a (5-ht1a) receptor-gi1 protein complex (Complex from Escherichia coli, Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (8 kDa, Protein from Homo sapiens)
- Buspirone (385 Da, Ligand)
- [(2r)-1-[oxidanyl-[(2r,3r,5s,6r)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5e,8e)-hexadeca-5,8,11,14-tetraenoate (854 Da, Ligand)
- Soluble cytochrome b562,5-hydroxytryptamine receptor 1a,5-hydroxytryptamine receptor 1a (61 kDa, Protein from Homo sapiens)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8ti1
Q-score: 0.419
Driggers CM, Kuo YY, Zhu P, ElSheikh A, Shyng SL
Nat Commun (2024) 15 pp. 2502-2502 [ Pubmed: 38509107 DOI: doi:10.1038/s41467-024-46751-5 ]
- Water (18 Da, Ligand)
- Kir6.2-q52r/sur1 open channel (880 kDa, Complex from Rattus norvegicus)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- [(2r)-1-octadecanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8z)-icosa-5,8,11,14-tetraenoate (1 kDa, Ligand)
- Sur1 (177 kDa, Protein from Mesocricetus auratus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Atp-sensitive inward rectifier potassium channel 11 (43 kDa, Protein from Rattus norvegicus)