Vitamin B12 transporter BtuB1 with lipoprotein BtuG1 from B. theta
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 8blw
Q-score: 0.449
Abellon-Ruiz J, Jana K, Silale A, Frey AM, Basle A, Trost M, Kleinekathofer U, van den Berg B
Nat Commun (2023) 14 pp. 4714-4714 [ Pubmed: 37543597 DOI: doi:10.1038/s41467-023-40427-2 ]
- Vitamin b12 transporter btub1 (78 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Complex of b. theta vitamin b12 transporter btub1 and lipoprotein btug1 (126 kDa, Complex from Bacteroides thetaiotaomicron VPI-5482)
- Ynce family protein (73 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Beta-d-galactopyranose (180 Da, Ligand)
BtuB3G3 bound to cyanocobalamin with disordered EL8
Resolution: 2.75 Å
EM Method: Single-particle
Fitted PDBs: 8p97
Q-score: 0.564
Abellon-Ruiz J, Jana K, Silale A, Frey AM, Basle A, Trost M, Kleinekathofer U, van den Berg B
Nat Commun (2023) 14 pp. 4714-4714 [ Pubmed: 37543597 DOI: doi:10.1038/s41467-023-40427-2 ]
- Cyanocobalamin (1 kDa, Ligand)
- Tonb-dependent receptor (78 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Putative surface layer protein (41 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Complex of tonb-dependent transporter btub3 with surface lipoprotein btug3 bound to cyanocobalamin (state 2) (122 kDa, Complex from Bacteroides thetaiotaomicron VPI-5482)
BtuB3G3 bound to cyanocobalamin with ordered EL8
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8p98
Q-score: 0.506
Abellon-Ruiz J, Jana K, Silale A, Frey AM, Basle A, Trost M, Kleinekathofer U, van den Berg B
Nat Commun (2023) 14 pp. 4714-4714 [ Pubmed: 37543597 DOI: doi:10.1038/s41467-023-40427-2 ]
- Cyanocobalamin (1 kDa, Ligand)
- Vitamin b12 transporter btub (81 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Putative surface layer protein (41 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Complex of tonb-dependent transporter btub3 with surface lipoprotein btug3 bound to cyanocobalamin (state 1) (122 kDa, Complex from Bacteroides thetaiotaomicron VPI-5482)
Substrate-free levan utilisation machinery (utilisome)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8a9y
Q-score: 0.458
White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Basle A, Trost M, Bolam DN, van den Berg B, Ranson NA
Nature (2023) 618 pp. 583-589 [ DOI: doi:10.1038/s41586-023-06146-w Pubmed: 37286596 ]
- Glycoside hydrolase family 32 (59 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Substrate-free levan utilisation machinery (utilisome) (Complex from Bacteroides thetaiotaomicron)
- Duf4960 domain-containing protein (50 kDa, Protein from Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
- Susc homolog (115 kDa, Protein from Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
- Magnesium ion (24 Da, Ligand)
Levan utilisation machinery (utilisome) with levan fructo-oligosaccharides DP 8-12
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8aa0
Q-score: 0.522
White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Basle A, Trost M, Bolam DN, van den Berg B, Ranson NA
Nature (2023) 618 pp. 583-589 [ DOI: doi:10.1038/s41586-023-06146-w Pubmed: 37286596 ]
- Glycoside hydrolase family 32 (59 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Levan utilisation machinery (utilisome) with levan fructo-oligosaccharides dp8-12 (Complex from Bacteroides thetaiotaomicron VPI-5482)
- Duf4960 domain-containing protein (50 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Susd homolog (66 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Susc homolog (115 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Magnesium ion (24 Da, Ligand)
Core SusCD transporter units from the levan utilisome with levan fructo-oligosaccharides DP 8-12
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8aa1
Q-score: 0.57
White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Basle A, Trost M, Bolam DN, van den Berg B, Ranson NA
Nature (2023) 618 pp. 583-589 [ DOI: doi:10.1038/s41586-023-06146-w Pubmed: 37286596 ]
- Magnesium ion (24 Da, Ligand)
- Levan utilisation machinery (utilisome) in the presence of levan fructo-oligosaccharides dp 8-12 (Complex from Bacteroides thetaiotaomicron VPI-5482)
- Susc homolog (115 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Susd homolog (66 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8aa2
Q-score: 0.529
White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Basle A, Trost M, Bolam DN, van den Berg B, Ranson NA
Nature (2023) 618 pp. 583-589 [ DOI: doi:10.1038/s41586-023-06146-w Pubmed: 37286596 ]
- Susd homolog (65 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Inactive levan utilisation machinery (utilisome) with levan fructo-oligosaccharides dp 15-25 (Complex from Bacteroides thetaiotaomicron VPI-5482)
- Duf4960 domain-containing protein (51 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Susc homolog (115 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Magnesium ion (24 Da, Ligand)
- Glycoside hydrolase family 32 (59 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8aa3
Q-score: 0.59
White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Basle A, Trost M, Bolam DN, van den Berg B, Ranson NA
Nature (2023) 618 pp. 583-589 [ DOI: doi:10.1038/s41586-023-06146-w Pubmed: 37286596 ]
- Susd homolog (65 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Magnesium ion (24 Da, Ligand)
- Susc homolog (115 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Inactive levan utilisation machinery (utilisome) in the presence of fructo-oligosaccharides dp 15-25 (Complex from Bacteroides thetaiotaomicron)
Consensus reconstruction of the dextran utilisation system
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8aa4
Q-score: 0.541
White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Basle A, Trost M, Bolam DN, van den Berg B, Ranson NA
Nature (2023) 618 pp. 583-589 [ DOI: doi:10.1038/s41586-023-06146-w Pubmed: 37286596 ]
T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8a8c
Q-score: 0.549
van den Berg B, Silale A, Basle A, Brandner AF, Mader SL, Khalid S
PNAS (2022) 119 pp. e2211672119-e2211672119 [ Pubmed: 36215462 DOI: doi:10.1073/pnas.2211672119 ]
- Ferrichrome outer membrane transporter/phage receptor (78 kDa, Protein from Escherichia coli K-12)
- Receptor-binding protein pb5 (69 kDa, Protein from Escherichia phage T5)
- T5 phage receptor-binding protein pb5 bound to ferrichrome transporter fhua (148 kDa, Complex from Escherichia phage T5)
- [(2r,3s,4r,5r,6r)-2-[[(2r,4r,5r,6r)-6-[(1r)-1,2-bis(oxidanyl)ethyl]-4-[(2r,4r,5r,6r)-6-[(1r)-1,2-bis(oxidanyl)ethyl]-2-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-carboxy-5-oxidanyl-oxan-2-yl]oxymethyl]-5-[[(3r)-3-dodecanoyloxytetradecanoyl]amino]-4-(3-nonanoyloxypropanoyloxy)-6-[[(2r,3s,4r,5r,6r)-3-oxidanyl-4-[(3s)-3-oxidanyltetradecanoyl]oxy-5-[[(3r)-3-oxidanyltridecanoyl]amino]-6-phosphonatooxy-oxan-2-yl]methoxy]oxan-3-yl] phosphate (1 kDa, Ligand)