Outer membrane attachment porin OmpM1 from Veillonella parvula
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8bym
Q-score: 0.562
Silale A, Zhu Y, Witwinowski J, Smith RE, Newman KE, Bhamidimarri SP, Basle A, Khalid S, Beloin C, Gribaldo S, van den Berg B
Nat Commun (2023) 14 pp. 7152-7152 [ Pubmed: 37932269 DOI: doi:10.1038/s41467-023-42601-y ]
Outer membrane attachment porin OmpM1 from Veillonella parvula, native
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 8bys
Q-score: 0.525
Silale A, Zhu Y, Witwinowski J, Smith RE, Newman KE, Bhamidimarri SP, Basle A, Khalid S, Beloin C, Gribaldo S, van den Berg B
Nat Commun (2023) 14 pp. 7152-7152 [ Pubmed: 37932269 DOI: doi:10.1038/s41467-023-42601-y ]
- Outer membrane attachment porin ompm1 trimer (130 kDa, Complex from Veillonella parvula)
- S-layer homology domain-containing protein (46 kDa, Protein from Veillonella parvula)
Outer membrane attachment porin OmpM1 from Veillonella parvula, C3 symmetry
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8byt
Q-score: 0.611
Silale A, Zhu Y, Witwinowski J, Smith RE, Newman KE, Bhamidimarri SP, Basle A, Khalid S, Beloin C, Gribaldo S, van den Berg B
Nat Commun (2023) 14 pp. 7152-7152 [ Pubmed: 37932269 DOI: doi:10.1038/s41467-023-42601-y ]
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 ]
- Beta-d-galactopyranose (180 Da, Ligand)
- Vitamin b12 transporter btub1 (78 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Ynce family protein (73 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)
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)
- 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)
- Tonb-dependent receptor (78 kDa, Protein 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 ]
- Complex of tonb-dependent transporter btub3 with surface lipoprotein btug3 bound to cyanocobalamin (state 1) (122 kDa, Complex from Bacteroides thetaiotaomicron VPI-5482)
- Vitamin b12 transporter btub (81 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Putative surface layer protein (41 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Cyanocobalamin (1 kDa, Ligand)
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 ]
- 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)
- Substrate-free levan utilisation machinery (utilisome) (Complex from Bacteroides thetaiotaomicron)
- Glycoside hydrolase family 32 (59 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Duf4960 domain-containing protein (50 kDa, Protein from Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
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 ]
- 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)
- Magnesium ion (24 Da, Ligand)
- Susc homolog (115 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Glycoside hydrolase family 32 (59 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
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 [ Pubmed: 37286596 DOI: doi:10.1038/s41586-023-06146-w ]
- 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 [ Pubmed: 37286596 DOI: doi:10.1038/s41586-023-06146-w ]
- Glycoside hydrolase family 32 (59 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- 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)
- Magnesium ion (24 Da, Ligand)
- Duf4960 domain-containing protein (51 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)
- Susc homolog (115 kDa, Protein from Bacteroides thetaiotaomicron VPI-5482)