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)
Resolution: 3.71 Å
EM Method: Single-particle
Fitted PDBs: 8q7r
Q-score: 0.324
Li J, Purser N, Liwocha J, Scott DC, Byers HA, Steigenberger B, Hill S, Tripathi-Giesgen I, Hinkle T, Hansen FM, Prabu JR, Radhakrishnan SK, Kirkpatrick DS, Reichermeier KM, Schulman BA, Kleiger G
Mol Cell (2024) 84 pp. 1304- [ DOI: doi:10.1016/j.molcel.2024.01.022 Pubmed: 38382526 ]
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Ubiquitin ligation to substrate by a cullin-ring e3 ligase & cdc34: nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2~donor ub-sil1 peptide (180 kDa, Complex)
- Cdc34, nedd8, elob, eloc, fem1c with ube2r2-donor ub-sil1 peptide (Complex from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Nucleotide exchange factor sil1 (2 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- 5-azanyl-1-oxidanyl-pentan-2-one (117 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8r5h
Q-score: 0.394
Li J, Purser N, Liwocha J, Scott DC, Byers HA, Steigenberger B, Hill S, Tripathi-Giesgen I, Hinkle T, Hansen FM, Prabu JR, Radhakrishnan SK, Kirkpatrick DS, Reichermeier KM, Schulman BA, Kleiger G
Mol Cell (2024) 84 pp. 1304- [ DOI: doi:10.1016/j.molcel.2024.01.022 Pubmed: 38382526 ]
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- 5-azanylpentan-2-one (101 Da, Ligand)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Bromodomain-containing protein 4 (13 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 r2 (25 kDa, Protein from Homo sapiens)
- Ubiquitin ligation to neosubstrate by a cullin-ring e3 ligase and cdc34: nedd8-cul2-rbx1-elob/c-vhl-mz1 with trapped ube2r2~donor ub-brd4 bd2 (190 kDa, Complex from Homo sapiens)
- Von hippel-lindau disease tumor suppressor (18 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- (2~{s},4~{r})-1-[(2~{s})-2-[2-[2-[2-[2-[2-[(9~{s})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{n}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide (1 kDa, Ligand)
- Cdc34, nedd8, elob, eloc, vhl, brd4 with ube2r2-donor ub- brd4 bd2 (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Resolution: 3.76 Å
EM Method: Single-particle
Fitted PDBs: 8pql
Q-score: 0.431
Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G
Nat Struct Mol Biol (2024) 31 pp. 378-389 [ Pubmed: 38326650 DOI: doi:10.1038/s41594-023-01206-1 ]
- 5-azanylpentan-2-one (101 Da, Ligand)
- Ring e3 ligase (rbx1) and cullin-2 (cul2) (Complex from Homo sapiens)
- Polyubiquitin-c,nucleotide exchange factor sil1 (79 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- K48-linked ubiquitin chain formation with a cullin-ring e3 ligase and cdc34:nedd8-cul2-rbx1-elob/c-fem1c with trapped ube2r2-donor ub-acceptor ub-sil1 peptide (190 kDa, Complex)
- E3 ubiquitin-protein ligase rbx1 (12 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Protein fem-1 homolog c (68 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Cdc34, nedd8, elob, eloc, fem1c with ube2r2-donor ub-acceptor ub-sil1 peptide and k48-linked ubiquitin chain (Complex from Homo sapiens)
- Ubiquitin (77 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 r2 (27 kDa, Protein from Homo sapiens)
Streptomycin and Hygromycin B bound to the 30S body
Resolution: 2.08 Å
EM Method: Single-particle
Fitted PDBs: 8cai
Q-score: 0.698
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ Pubmed: 37550453 DOI: doi:10.1038/s41594-023-01047-y ]
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
- Potassium ion (39 Da, Ligand)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein bs6, non-modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
- Hygromycin b variant (527 Da, Ligand)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- Spectinomycin (332 Da, Ligand)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- [(2~{s},3~{s},4~{s},5~{r},6~{s})-2-[(2~{r},3~{r},4~{r},5~{s})-2-[(1~{r},2~{s},3~{r},4~{r},5~{s},6~{r})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium (602 Da, Ligand)
Streptomycin bound to the 30S body
Resolution: 1.79 Å
EM Method: Single-particle
Fitted PDBs: 8cgj
Q-score: 0.729
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ Pubmed: 37550453 DOI: doi:10.1038/s41594-023-01047-y ]
- Potassium ion (39 Da, Ligand)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein bs6, non-modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
- Tetracycline (444 Da, Ligand)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
- [(2~{s},3~{s},4~{s},5~{r},6~{s})-2-[(2~{r},3~{r},4~{r},5~{s})-2-[(1~{r},2~{s},3~{r},4~{r},5~{s},6~{r})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium (602 Da, Ligand)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
Gentamicin bound to the 30S body
Resolution: 1.89 Å
EM Method: Single-particle
Fitted PDBs: 8cgu
Q-score: 0.76
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ Pubmed: 37550453 DOI: doi:10.1038/s41594-023-01047-y ]
- Potassium ion (39 Da, Ligand)
- (2r,3r,4r,5r)-2-((1s,2s,3r,4s,6r)-4,6-diamino-3-((2r,3r,6s)-3-amino-6-(aminomethyl)-tetrahydro-2h-pyran-2-yloxy)-2-hydr oxycyclohexyloxy)-5-methyl-4-(methylamino)-tetrahydro-2h-pyran-3,5-diol (449 Da, Ligand)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein bs6, non-modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8ayl
Q-score: 0.511
Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson JF, Cais O, Nakagawa T, Greger IH
Nat Commun (2023) 14 pp. 1659-1659 [ DOI: doi:10.1038/s41467-023-37259-5 Pubmed: 36966141 ]
- Palmitic acid (256 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2h)-yl]methyl}phosphonic acid (409 Da, Ligand)
- Isoform flip of glutamate receptor 2 (96 kDa, Protein from Rattus norvegicus)
- 5-[2-(4-fluorophenyl)-7-(4-oxidanylpiperidin-1-yl)pyrazolo[1,5-c]pyrimidin-3-yl]-1,3-dihydroindol-2-one (443 Da, Ligand)
- (2r)-2,3-dihydroxypropyl (9z)-octadec-9-enoate (356 Da, Ligand)
- Resting state glua1/a2 ampa receptor in complex with tarp gamma 8 and ligand jnj-61432059 (Complex from Rattus)
- Voltage-dependent calcium channel gamma-8 subunit (43 kDa, Protein from Rattus norvegicus)
- Isoform flip of glutamate receptor 1 (102 kDa, Protein from Rattus norvegicus)
Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-55511118
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8aym
Q-score: 0.472
Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson JF, Cais O, Nakagawa T, Greger IH
Nat Commun (2023) 14 pp. 1659-1659 [ DOI: doi:10.1038/s41467-023-37259-5 Pubmed: 36966141 ]
- Palmitic acid (256 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2h)-yl]methyl}phosphonic acid (409 Da, Ligand)
- Isoform flip of glutamate receptor 2 (96 kDa, Protein from Rattus norvegicus)
- (2r)-2,3-dihydroxypropyl (9z)-octadec-9-enoate (356 Da, Ligand)
- 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1h-benzimidazol-2-ol (328 Da, Ligand)
- Glua1/a2 ampa receptor in complex with tarp gamma 8 and ligand jnj-55511118 (Complex from Rattus norvegicus)
- Voltage-dependent calcium channel gamma-8 subunit (43 kDa, Protein from Rattus norvegicus)
- Isoform flip of glutamate receptor 1 (102 kDa, Protein from Rattus norvegicus)
Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand LY3130481
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8ayn
Q-score: 0.558
Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson JF, Cais O, Nakagawa T, Greger IH
Nat Commun (2023) 14 pp. 1659-1659 [ DOI: doi:10.1038/s41467-023-37259-5 Pubmed: 36966141 ]
- Palmitic acid (256 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2h)-yl]methyl}phosphonic acid (409 Da, Ligand)
- 6-[(1~{s})-1-[1-[5-(2-hydroxyethyloxy)pyridin-2-yl]pyrazol-3-yl]ethyl]-3~{h}-1,3-benzothiazol-2-one (382 Da, Ligand)
- Isoform flip of glutamate receptor 2 (96 kDa, Protein from Rattus norvegicus)
- (2r)-2,3-dihydroxypropyl (9z)-octadec-9-enoate (356 Da, Ligand)
- Glua1/a2 ampa receptor in complex with tarp gamma 8 and ligand ly3130481 (Complex from Rattus norvegicus)
- Voltage-dependent calcium channel gamma-8 subunit (43 kDa, Protein from Rattus norvegicus)
- Isoform flip of glutamate receptor 1 (102 kDa, Protein from Rattus norvegicus)