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 ]
- S-layer homology domain-containing protein (46 kDa, Protein from Veillonella parvula)
- Outer membrane attachment porin ompm1 trimer (130 kDa, Complex 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 ]
MTHFR + SAH symmetric dis-inhibited state
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8qa4
Q-score: 0.536
Blomgren LKM, Huber M, Mackinnon SR, Burer C, Basle A, Yue WW, Froese DS, McCorvie TJ
Nat Commun (2024) 15 pp. 3248-3248 [ DOI: doi:10.1038/s41467-024-47174-y Pubmed: 38622112 ]
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Water (18 Da, Ligand)
- Human 5,10-methylenetetrahydrofolate reductase in complex with s-adenosyl-l-homocysteine, regulatory domains (150 kDa, Complex from Homo sapiens)
- Methylenetetrahydrofolate reductase (nadph) (75 kDa, Protein from Homo sapiens)
MTHFR + SAH asymmetric dis-inhibited state
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8qa5
Q-score: 0.358
Blomgren LKM, Huber M, Mackinnon SR, Burer C, Basle A, Yue WW, Froese DS, McCorvie TJ
Nat Commun (2024) 15 pp. 3248-3248 [ DOI: doi:10.1038/s41467-024-47174-y Pubmed: 38622112 ]
- Human 5,10-methylenetetrahydrofolate reductase in complex with s-adenosyl-l-homocysteine, regulatory domains with one catalytic domain (150 kDa, Complex from Homo sapiens)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Methylenetetrahydrofolate reductase (nadph) (75 kDa, Protein from Homo sapiens)
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8qa6
Q-score: 0.535
Blomgren LKM, Huber M, Mackinnon SR, Burer C, Basle A, Yue WW, Froese DS, McCorvie TJ
Nat Commun (2024) 15 pp. 3248-3248 [ DOI: doi:10.1038/s41467-024-47174-y Pubmed: 38622112 ]
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Human 5,10-methylenetetrahydrofolate reductase in complex with s-adenosyl-l-methionine (150 kDa, Complex from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- Methylenetetrahydrofolate reductase (nadph) (75 kDa, Protein from Homo sapiens)
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))