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.
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 [ Pubmed: 38172635 DOI: doi:10.1038/s41586-023-06799-7 ]
- 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 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)
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 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 [ Pubmed: 38172635 DOI: doi:10.1038/s41586-023-06799-7 ]
- (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)
- 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)
- 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)
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 [ Pubmed: 38172635 DOI: doi:10.1038/s41586-023-06799-7 ]
- 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)
- Lipopolysaccharide export system permease protein lptf (41 kDa, Protein from Acinetobacter baylyi ADP1)
- Lipopolysaccharide export system atp-binding protein lptb (27 kDa, Protein from Acinetobacter baylyi ADP1)
- Lps export abc transporter permease lptg (40 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 [ 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: 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 [ 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-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)
- (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)
- 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)
Local refinement of MceG in Msmeg Mce1 transporter (Map0a)
Chen J, Fruhauf A, Fan C, Ponce J, Ueberheide B, Bhabha G, Ekiert DC
Nature (2023) 620 pp. 445-452 [ DOI: doi:10.1038/s41586-023-06366-0 Pubmed: 37495693 ]
- Virulence factor mce family protein mce1a (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1d (Protein from Mycolicibacterium smegmatis MC2 155)
- Mce1 lipid transporter composed of mce1 mce proteins (mce1abcdef) and an abc transporter (yrbe1a-b, 2 copies of mceg) (Complex from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1c (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1e (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1b (Protein from Mycolicibacterium smegmatis MC2 155)
- Abc transporter permease protein yrbe1b (Protein from Mycolicibacterium smegmatis MC2 155)
- Abc transporter permease protein yrbe1a (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1f (Protein from Mycolicibacterium smegmatis MC2 155)
- Atp-binding protein mceg (Protein from Mycolicibacterium smegmatis MC2 155)
Local refinement of YrbE and MCE ring in Msmeg Mce1 transporter (Map0b)
Chen J, Fruhauf A, Fan C, Ponce J, Ueberheide B, Bhabha G, Ekiert DC
Nature (2023) 620 pp. 445-452 [ DOI: doi:10.1038/s41586-023-06366-0 Pubmed: 37495693 ]
- Virulence factor mce family protein mce1a (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1d (Protein from Mycolicibacterium smegmatis MC2 155)
- Mce1 lipid transporter composed of mce1 mce proteins (mce1abcdef) and an abc transporter (yrbe1a-b, 2 copies of mceg) (Complex from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1c (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1e (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1b (Protein from Mycolicibacterium smegmatis MC2 155)
- Abc transporter permease protein yrbe1b (Protein from Mycolicibacterium smegmatis MC2 155)
- Abc transporter permease protein yrbe1a (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1f (Protein from Mycolicibacterium smegmatis MC2 155)
- Atp-binding protein mceg (Protein from Mycolicibacterium smegmatis MC2 155)
Local refinement of MCE ring and needle in Msmeg Mce1 transporter (Map0c)
Chen J, Fruhauf A, Fan C, Ponce J, Ueberheide B, Bhabha G, Ekiert DC
Nature (2023) 620 pp. 445-452 [ DOI: doi:10.1038/s41586-023-06366-0 Pubmed: 37495693 ]
- Virulence factor mce family protein mce1a (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1d (Protein from Mycolicibacterium smegmatis MC2 155)
- Mce1 lipid transporter composed of mce1 mce proteins (mce1abcdef) and an abc transporter (yrbe1a-b, 2 copies of mceg) (Complex from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1c (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1e (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1b (Protein from Mycolicibacterium smegmatis MC2 155)
- Abc transporter permease protein yrbe1b (Protein from Mycolicibacterium smegmatis MC2 155)
- Abc transporter permease protein yrbe1a (Protein from Mycolicibacterium smegmatis MC2 155)
- Virulence factor mce family protein mce1f (Protein from Mycolicibacterium smegmatis MC2 155)
- Atp-binding protein mceg (Protein from Mycolicibacterium smegmatis MC2 155)