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 ]
- Abc transporter (147 MDa, Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Spermidine/putrescine import atp-binding protein pota (40 kDa, Protein from Escherichia coli)
- Spermidine/putrescine abc transporter permease potb (30 kDa, Protein from Escherichia coli)
- Spermidine/putrescine import atp-binding protein pota (41 kDa, Protein from Escherichia coli)
- Spermidine (145 Da, Ligand)
- Spermidine/putrescine transport system permease protein potc (27 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 [ Pubmed: 38172635 DOI: doi:10.1038/s41586-023-06799-7 ]
- Lipopolysaccharide export system permease protein lptf (41 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)
- Lipopolysaccharide export system atp-binding protein lptb (29 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)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 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)
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 [ Pubmed: 38172635 DOI: doi:10.1038/s41586-023-06799-7 ]
- Zosurabalpin (790 Da, Ligand)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
- Lps export abc transporter permease lptg (40 kDa, Protein from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system atp-binding protein lptb (29 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)
- Dodecyl-beta-d-maltoside (510 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)
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 [ Pubmed: 38172635 DOI: doi:10.1038/s41586-023-06799-7 ]
- (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)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
- Inner membrane lipopolysaccharide transporter composed of lptf, lptg, and two molecules of lptb in complex with lipopolysaccharide (139 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 (29 kDa, Protein from Acinetobacter baylyi ADP1)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
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 [ Pubmed: 37619560 DOI: doi:10.1016/j.str.2023.07.014 ]
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 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)
- Trehalose-specific importer lpqy-sugabc complex (Complex from Mycolicibacterium smegmatis MC2 155)
- Bacterial extracellular solute-binding protein (50 kDa, Protein 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 [ Pubmed: 37619560 DOI: doi:10.1016/j.str.2023.07.014 ]
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 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)
- Trehalose-specific importer lpqy-sugabc complex (Complex from Mycolicibacterium smegmatis MC2 155)
- Bacterial extracellular solute-binding protein (50 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Resolution: 4.55 Å
EM Method: Single-particle
Fitted PDBs: 8hpn
Q-score: 0.249
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 [ Pubmed: 37619560 DOI: doi:10.1016/j.str.2023.07.014 ]
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 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)
- Trehalose-specific importer lpqy-sugabc complex (Complex from Mycolicibacterium smegmatis MC2 155)
- Bacterial extracellular solute-binding protein (50 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Resolution: 3.75 Å
EM Method: Single-particle
Fitted PDBs: 8hpr
Q-score: 0.369
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 [ Pubmed: 37619560 DOI: doi:10.1016/j.str.2023.07.014 ]
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 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)
- Trehalose-specific importer lpqy-sugabc complex (Complex from Mycolicibacterium smegmatis MC2 155)
- Bacterial extracellular solute-binding protein (50 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 8hps
Q-score: 0.412
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 [ Pubmed: 37619560 DOI: doi:10.1016/j.str.2023.07.014 ]
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 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)
- Trehalose-specific importer lpqy-sugabc complex (Complex from Mycolicibacterium smegmatis MC2 155)
- Bacterial extracellular solute-binding protein (50 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
ABC transporter NosDFY, nucleotide-free in lipid nanodisc
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7o13
Q-score: 0.403
Muller C, Zhang L, Zipfel S, Topitsch A, Lutz M, Eckert J, Prasser B, Chami M, Lu W, Du J, Einsle O
Nature (2022) 608 pp. 626-631 [ Pubmed: 35896743 DOI: doi:10.1038/s41586-022-05015-2 ]
- Probable abc transporter binding protein nosd (48 kDa, Protein from Pseudomonas stutzeri ATCC 14405 = CCUG 16156)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Probable abc transporter atp-binding protein nosf (33 kDa, Protein from Pseudomonas stutzeri ATCC 14405 = CCUG 16156)
- Abc transporter nosfy in complex with accessory periplasmic protein nosd (Complex from Pseudomonas stutzeri ATCC 14405 = CCUG 16156)
- Probable abc transporter permease protein nosy (29 kDa, Protein from Pseudomonas stutzeri ATCC 14405 = CCUG 16156)