Cryo-EM structure of E.coli spermidine transporter PotABC with spermidine
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8y5g
Q-score: 0.509
Qiao Z, Do PH, Yeo JY, Ero R, Li Z, Zhan L, Basak S, Gao YG
Sci Adv (2024) 10 pp. eado8107-eado8107 [ DOI: doi:10.1126/sciadv.ado8107 Pubmed: 39303029 ]
- Spermidine/putrescine import atp-binding protein pota (40 kDa, Protein from Escherichia coli)
- Abc transporter (147 MDa, Complex from Escherichia coli)
- Spermidine/putrescine transport system permease protein potc (27 kDa, Protein from Escherichia coli)
- Spermidine (145 Da, Ligand)
- Spermidine/putrescine abc transporter permease potb (30 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Spermidine/putrescine import atp-binding protein pota (41 kDa, Protein from Escherichia coli)
Acinetobacter baylyi LptB2FG bound to lipopolysaccharide and a macrocyclic peptide
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8frl
Q-score: 0.546
Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D
Nature (2024) 625 pp. 572-577 [ DOI: doi:10.1038/s41586-023-06799-7 Pubmed: 38172635 ]
- Inner membrane lipopolysaccharide transporter composed of lptf, lptg and two molecules of lptb in complex with lipopolysaccharide and a macrocyclic peptide. (139 kDa, Complex from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system atp-binding protein lptb (29 kDa, Protein from Acinetobacter baylyi ADP1)
- (7s,10s,13s,17p)-10-(4-aminobutyl)-7-(3-aminopropyl)-17-(6-aminopyridin-3-yl)-20-chloro-13-[(1h-indol-3-yl)methyl]-12-methyl-6,7,9,10,12,13,15,16-octahydropyrido[2,3-b][1,5,8,11,14]benzothiatetraazacycloheptadecine-8,11,14(5h)-trione (797 Da, Ligand)
- Lps export abc transporter permease lptg (40 kDa, Protein from Acinetobacter baylyi ADP1)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
- (2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-[(2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-5-[(2~{s},3~{s},4~{r},5~{r},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-4-[(2~{r},3~{s},4~{r},5~{s},6~{r})-6-[(1~{s})-2-[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-5-[[(3~{r})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-3-oxidanyl-5-[[(3~{r})-3-oxidanyltetradecanoyl]amino]-4-[(3~{r})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{r})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid (2 kDa, Ligand)
Acinetobacter baylyi LptB2FG bound to lipopolysaccharide.
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8frm
Q-score: 0.518
Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D
Nature (2024) 625 pp. 572-577 [ DOI: doi:10.1038/s41586-023-06799-7 Pubmed: 38172635 ]
- Inner membrane lipopolysaccharide transporter composed of lptf, lptg and two molecules of lptb in complex with lipopolysaccharide. (139 kDa, Complex from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system atp-binding protein lptb (29 kDa, Protein from Acinetobacter baylyi ADP1)
- Lps export abc transporter permease lptg (40 kDa, Protein from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
- (2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-[(2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-5-[(2~{s},3~{s},4~{r},5~{r},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-4-[(2~{r},3~{s},4~{r},5~{s},6~{r})-6-[(1~{s})-2-[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-5-[[(3~{r})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-3-oxidanyl-5-[[(3~{r})-3-oxidanyltetradecanoyl]amino]-4-[(3~{r})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{r})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid (2 kDa, Ligand)
Acinetobacter baylyi LptB2FG bound to lipopolysaccharide and RG6006
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8frn
Q-score: 0.46
Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D
Nature (2024) 625 pp. 572-577 [ DOI: doi:10.1038/s41586-023-06799-7 Pubmed: 38172635 ]
- Zosurabalpin (790 Da, Ligand)
- Inner membrane lipopolysaccharide transporter composed of lptf, lptg and two molecules of lptb in complex with lipopolysaccharide and zosurabalpin (139 kDa, Complex from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system atp-binding protein lptb (29 kDa, Protein from Acinetobacter baylyi ADP1)
- Lps export abc transporter permease lptg (40 kDa, Protein from Acinetobacter baylyi ADP1)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
- (2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-[(2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-5-[(2~{s},3~{s},4~{r},5~{r},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-4-[(2~{r},3~{s},4~{r},5~{s},6~{r})-6-[(1~{s})-2-[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-5-[[(3~{r})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-3-oxidanyl-5-[[(3~{r})-3-oxidanyltetradecanoyl]amino]-4-[(3~{r})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{r})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid (2 kDa, Ligand)
Acinetobacter baylyi LptB2FG bound to lipopolysaccharide and a macrocyclic peptide
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8fro
Q-score: 0.512
Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D
Nature (2024) 625 pp. 572-577 [ DOI: doi:10.1038/s41586-023-06799-7 Pubmed: 38172635 ]
- Inner membrane lipopolysaccharide transporter composed of lptf, lptg and two molecules of lptb in complex with lipopolysaccharide and a macrocyclic peptide. (139 kDa, Complex from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system atp-binding protein lptb (29 kDa, Protein from Acinetobacter baylyi ADP1)
- (7s,10s,13s)-10-(4-aminobutyl)-7-(3-aminopropyl)-17,20-dichloro-13-[(1h-indol-3-yl)methyl]-12-methyl-6,7,9,10,12,13,15,16-octahydropyrido[2,3-b][1,5,8,11,14]benzothiatetraazacycloheptadecine-8,11,14(5h)-trione (739 Da, Ligand)
- Lps export abc transporter permease lptg (40 kDa, Protein from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
- (2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-[(2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-5-[(2~{s},3~{s},4~{r},5~{r},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-4-[(2~{r},3~{s},4~{r},5~{s},6~{r})-6-[(1~{s})-2-[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-5-[[(3~{r})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-3-oxidanyl-5-[[(3~{r})-3-oxidanyltetradecanoyl]amino]-4-[(3~{r})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{r})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid (2 kDa, Ligand)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8frp
Q-score: 0.383
Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D
Nature (2024) 625 pp. 572-577 [ DOI: doi:10.1038/s41586-023-06799-7 Pubmed: 38172635 ]
- Lipopolysaccharide export system protein lptc (1 kDa, Protein from Acinetobacter baylyi ADP1)
- Inner membrane lipopolysaccharide transporter composed of lptf, lptg, lptc and two molecules of lptb. (159 kDa, Complex from Acinetobacter baylyi ADP1)
- Lps export abc transporter permease lptg (40 kDa, Protein from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system atp-binding protein lptb (27 kDa, Protein from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
Acinetobacter baylyi LptB2FG bound to Acinetobacter baylyi lipopolysaccharide
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8ufg
Q-score: 0.527
Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D
Nature (2024) 625 pp. 572-577 [ DOI: doi:10.1038/s41586-023-06799-7 Pubmed: 38172635 ]
- (2~{r},4~{r},5~{r},6~{r})-2-[(2~{r},4~{r},5~{r},6~{r})-5-[(2~{s},4~{r},5~{r},6~{r})-4-[(2~{r},3~{r},4~{r},5~{s},6~{s})-3-acetamido-6-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-carboxy-5-oxidanyl-oxan-2-yl]oxy-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-4-[(3~{s})-3-dodecanoyloxydodecanoyl]oxy-6-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-5-[[(3~{r})-3-heptanoyloxyundecanoyl]amino]-3-oxidanyl-4-[(3~{r})-3-oxidanyloctanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-5-[[(3~{s})-3-[(3~{r})-3-oxidanyldecanoyl]oxydecanoyl]amino]-3-phosphonooxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-4,5-bis(oxidanyl)oxane-2-carboxylic acid (2 kDa, Ligand)
- Inner membrane lipopolysaccharide transporter composed of lptf, lptg, and two molecules of lptb in complex with lipopolysaccharide (139 kDa, Complex from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system atp-binding protein lptb (29 kDa, Protein from Acinetobacter baylyi ADP1)
- Lps export abc transporter permease lptg (40 kDa, Protein from Acinetobacter baylyi ADP1)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8ufh
Q-score: 0.519
Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D
Nature (2024) 625 pp. 572-577 [ DOI: doi:10.1038/s41586-023-06799-7 Pubmed: 38172635 ]
- Lipopolysaccharide export system atp-binding protein lptb (29 kDa, Protein from Acinetobacter baylyi ADP1)
- Inner membrane lipopolysaccharide transporter composed of lptf, lptg, and two molecules of lptb in complex with lipopolysaccharide and a macrocyclic peptide (139 kDa, Complex from Acinetobacter baylyi ADP1)
- (7s,10s,13s,17p)-10-(4-aminobutyl)-7-(3-aminopropyl)-17-(6-aminopyridin-3-yl)-20-chloro-13-[(1h-indol-3-yl)methyl]-12-methyl-6,7,9,10,12,13,15,16-octahydropyrido[2,3-b][1,5,8,11,14]benzothiatetraazacycloheptadecine-8,11,14(5h)-trione (797 Da, Ligand)
- Lps export abc transporter permease lptg (40 kDa, Protein from Acinetobacter baylyi ADP1)
- (2~{r},4~{r},5~{r},6~{r})-2-[(2~{r},4~{r},5~{r},6~{r})-5-[(2~{s},4~{r},5~{r},6~{r})-4-[(2~{r},3~{r},4~{r},5~{s},6~{s})-3-acetamido-6-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-carboxy-5-oxidanyl-oxan-2-yl]oxy-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-4-[(3~{s})-3-dodecanoyloxydodecanoyl]oxy-6-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-5-[[(3~{r})-3-heptanoyloxynonanoyl]amino]-3-oxidanyl-4-[(3~{r})-3-oxidanyloctanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-5-[[(3~{s})-3-[(3~{r})-3-oxidanyldodecanoyl]oxydecanoyl]amino]-3-phosphonooxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-4,5-bis(oxidanyl)oxane-2-carboxylic acid (2 kDa, Ligand)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
Resolution: 4.29 Å
EM Method: Single-particle
Fitted PDBs: 8hpl
Q-score: 0.292
Liang J, Yang X, Hu T, Gao Y, Yang Q, Yang H, Peng W, Zhou X, Guddat LW, Zhang B, Rao Z, Liu F
Structure (2023) 31 pp. 1158-1165.e3 [ DOI: doi:10.1016/j.str.2023.07.014 Pubmed: 37619560 ]
- Abc transporter, permease protein sugb (29 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Abc transporter, atp-binding protein sugc (43 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Bacterial extracellular solute-binding protein (50 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Trehalose-specific importer lpqy-sugabc complex (Complex from Mycolicibacterium smegmatis MC2 155)
Resolution: 3.82 Å
EM Method: Single-particle
Fitted PDBs: 8hpm
Q-score: 0.347
Liang J, Yang X, Hu T, Gao Y, Yang Q, Yang H, Peng W, Zhou X, Guddat LW, Zhang B, Rao Z, Liu F
Structure (2023) 31 pp. 1158-1165.e3 [ DOI: doi:10.1016/j.str.2023.07.014 Pubmed: 37619560 ]
- Abc transporter, permease protein sugb (29 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Abc transporter, atp-binding protein sugc (43 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Bacterial extracellular solute-binding protein (50 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Trehalose-specific importer lpqy-sugabc complex (Complex from Mycolicibacterium smegmatis MC2 155)