structure of a membrane-bound glycosyltransferase
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7xe4
Q-score: 0.471
Hu X, Yang P, Chai C, Liu J, Sun H, Wu Y, Zhang M, Zhang M, Liu X, Yu H
Nature (2023) 616 pp. 190-198 [ DOI: doi:10.1038/s41586-023-05856-5 Pubmed: 36949198 ]
- Dodecane (170 Da, Ligand)
- Membrane-bound glycosyltransferase (215 kDa, Complex from Saccharomyces cerevisiae)
- 1,3-beta-glucan synthase component fks1 (215 kDa, Protein from Saccharomyces cerevisiae)
- (11r,14s)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate (495 Da, Ligand)
- Decane (142 Da, Ligand)
- Tetradecane (198 Da, Ligand)
- Nonane (128 Da, Ligand)
- Heptane (100 Da, Ligand)
Structure of a mutated membrane-bound glycosyltransferase
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7yuy
Q-score: 0.494
Hu X, Yang P, Chai C, Liu J, Sun H, Wu Y, Zhang M, Zhang M, Liu X, Yu H
Nature (2023) 616 pp. 190-198 [ DOI: doi:10.1038/s41586-023-05856-5 Pubmed: 36949198 ]
- Dodecane (170 Da, Ligand)
- 1,3-beta-glucan synthase component fks1 (215 kDa, Protein from Saccharomyces cerevisiae)
- Membrane-bound glycosyltransferase (215 kDa, Complex from Saccharomyces cerevisiae)
- (11r,14s)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate (495 Da, Ligand)
- Decane (142 Da, Ligand)
- Tetradecane (198 Da, Ligand)
- Nonane (128 Da, Ligand)
- Heptane (100 Da, Ligand)
Alpha1/BetaB Heteromeric Glycine Receptor in 1 mM Glycine 20 uM Ivermectin State
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8fe1
Q-score: 0.527
Gibbs E, Klemm E, Seiferth D, Kumar A, Ilca SL, Biggin PC, Chakrapani S
Nat Commun (2023) 14 pp. 1363-1363 [ Pubmed: 36914669 DOI: doi:10.1038/s41467-023-37106-7 ]
- Palmitic acid (256 Da, Ligand)
- Glycine receptor subunit alphaz1 (52 kDa, Protein from Danio rerio)
- 1,2-dimyristoyl-sn-glycero-3-phosphocholine (678 Da, Ligand)
- Glycine receptor beta subunit 2 (65 kDa, Protein from Danio rerio)
- Decane (142 Da, Ligand)
- Glycine (75 Da, Ligand)
- (2ae,4e,5's,6s,6'r,7s,8e,11r,13r,15s,17ar,20r,20ar,20bs)-6'-[(2s)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2h,7h-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-o-(2,6-dideoxy-3-o-methyl-alpha-l-arabino-hexopyranosyl)-3-o-methyl-alpha-l-arabino-hexopyranoside (875 Da, Ligand)
- Zebrafish alpha1 betab heteromeric glycine receptor (250 kDa, Complex from Danio rerio)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 8b01
Q-score: 0.539
Davies JS, Currie MJ, North RA, Scalise M, Wright JD, Copping JM, Remus DM, Gulati A, Morado DR, Jamieson SA, Newton-Vesty MC, Abeysekera GS, Ramaswamy S, Friemann R, Wakatsuki S, Allison JR, Indiveri C, Drew D, Mace PD, Dobson RCJ
Nat Commun (2023) 14 pp. 1120-1120 [ Pubmed: 36849793 DOI: doi:10.1038/s41467-023-36590-1 ]
- Tridecane (184 Da, Ligand)
- Siaqm with megabody (Complex)
- Phosphatidylethanolamine (734 Da, Ligand)
- Hexane (86 Da, Ligand)
- Docosane (310 Da, Ligand)
- N-octane (114 Da, Ligand)
- Megabody (Complex from Helicobacter pylori)
- Decane (142 Da, Ligand)
- Putative trap-type c4-dicarboxylate transport system, small permease component (19 kDa, Protein from Photobacterium profundum SS9)
- Siaqm (Complex from Photobacterium profundum)
- Megabody c7hopq (54 kDa, Protein from synthetic construct)
- Putative trap-type c4-dicarboxylate transport system, large permease component (45 kDa, Protein from Photobacterium profundum SS9)
- Sodium ion (22 Da, Ligand)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7qn5
Q-score: 0.58
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- N-octane (114 Da, Ligand)
- Nanobody nb25 (13 kDa, Protein from Lama glama)
- Decane (142 Da, Ligand)
- Human full-length extrasynaptic alpha4beta3delta gaba(a)r in complex with nanobody nb25 (Complex from Homo sapiens)
- 1,2-dipalmitoyl-sn-glycero-3-phosphate (647 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit alpha-4 (61 kDa, Protein from Homo sapiens)
- Chloride ion (35 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit delta (52 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (238 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7qn7
Q-score: 0.548
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Histamine (111 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hexadecane (226 Da, Ligand)
- Water (18 Da, Ligand)
- Human full-length extrasynaptic alpha4beta3delta gaba(a)r in complex with gaba, histamine and nanobody nb25 (Complex from Homo sapiens)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Decane (142 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit alpha-4 (61 kDa, Protein from Homo sapiens)
- Gamma-aminobutyric acid receptor subunit delta (52 kDa, Protein from Homo sapiens)
- 1,2-dipalmitoyl-sn-glycero-3-phosphate (647 Da, Ligand)
- Nanobody nb25 (13 kDa, Protein from Homo sapiens)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7qn9
Q-score: 0.505
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Human full-length extrasynaptic alpha4beta3delta gaba(a)r in complex with histamine and nanobody nb25 (Complex from Homo sapiens)
- Histamine (111 Da, Ligand)
- Hexadecane (226 Da, Ligand)
- Decane (142 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit alpha-4 (61 kDa, Protein from Homo sapiens)
- Gamma-aminobutyric acid receptor subunit delta (52 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Nanobody nb25 (13 kDa, Protein from Homo sapiens)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7qnc
Q-score: 0.523
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Histamine (111 Da, Ligand)
- Human full-length extrasynaptic alpha4beta3delta gaba(a)r in complex with thip (gaboxadol), histamine and nanobody nb25 (Complex from Homo sapiens)
- Nanobody nb25 (13 kDa, Protein from Lama glama)
- Decane (142 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit alpha-4 (61 kDa, Protein from Homo sapiens)
- 4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one (140 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit delta (52 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7qne
Q-score: 0.606
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Gaba(a) receptor subunit alpha-1 (51 kDa, Protein from Homo sapiens)
- N-octane (114 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Decane (142 Da, Ligand)
- Megabody mb38 (13 kDa, Protein from Lama glama)
- Ethyl 8-[(azanylidene-$l^{4}-azanylidene)amino]-5-methyl-6-oxidanylidene-4~{h}-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate (326 Da, Ligand)
- Gaba(a) receptor subunit gamma-2 (56 kDa, Protein from Homo sapiens)
- Human full-length synaptic alpha1beta3gamma2 gaba(a)r in complex with ro15-4513 and megabody mb38 (Complex from Homo sapiens)
Transport protein in an occluded state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7m5v
Q-score: 0.49
Tillinghast J, Drury S, Bowser D, Benn A, Lee KPK
Mol Cell (2021) 81 pp. 4650-4662.e4 [ Pubmed: 34715014 DOI: doi:10.1016/j.molcel.2021.10.002 ]
- Dodecane (170 Da, Ligand)
- (2r)-3-{[(s)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate (746 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Transport protein in an occluded state (130 kDa, Complex from Homo sapiens)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Decane (142 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- 1-dodecanol (186 Da, Ligand)
- Polyamine-transporting atpase 13a2 (129 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)