The CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis
Resolution: 1.85 Å
EM Method: Single-particle
Fitted PDBs: 8uem
Q-score: 0.777
Kropp A, Gillett DL, Venugopal H, Gonzalvez MA, Lingford JP, Jain S, Barlow CK, Zhang J, Greening C, Grinter R
Nat Chem Biol (2025) [ DOI: doi:10.1038/s41589-025-01836-0 Pubmed: 39881213 ]
- Carbon monoxide dehydrogenase (large chain), coxl (85 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Pterin cytosine dinucleotide (696 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Mocu carbon monoxide dehydrogenase (mocu-codh) (270 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Water (18 Da, Ligand)
- [2fe-2s] binding domain protein (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cu(i)-s-mo(iv)(=o)oh cluster (224 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Carbon monoxide dehydrogenase medium chain (31 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of PqqU with ligand PQQ
Resolution: 1.99 Å
EM Method: Single-particle
Fitted PDBs: 9c4o
Q-score: 0.74
Munder F, Voutsinos M, Hantke K, Venugopal H, Grinter R
To Be Published
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Pyrroloquinoline quinone (330 Da, Ligand)
- Pyrroloquinoline quinone transporter (78 kDa, Protein from Escherichia coli BW25113)
- Complex of pqqu with pqq (78 kDa, Complex from Escherichia coli BW25113)
Resolution: 2.19 Å
EM Method: Single-particle
Fitted PDBs: 7utd
Q-score: 0.496
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ Pubmed: 36890228 DOI: doi:10.1038/s41586-023-05781-7 ]
- Type 2 [nife]-hydrogenase huc membrane adapter subunit (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- Nickel (iii) ion (58 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Hydrogenase-2, small subunit (39 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
Resolution: 1.67 Å
EM Method: Single-particle
Fitted PDBs: 7uur
Q-score: 0.837
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ DOI: doi:10.1038/s41586-023-05781-7 Pubmed: 36890228 ]
- Water (18 Da, Ligand)
- Menadione (172 Da, Ligand)
- Hydrogenase-2, small subunit (35 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nickel (iii) ion (58 Da, Ligand)
- Hydroxide ion (17 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 7uus
Q-score: 0.104
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ Pubmed: 36890228 DOI: doi:10.1038/s41586-023-05781-7 ]
- Menaquinone-9 (785 Da, Ligand)
- Nickel (iii) ion (58 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Hydrogenase-2, small subunit (39 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- [nife]-hydrogenase huc membrane associated subunit (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
Resolution: 1.52 Å
EM Method: Single-particle
Fitted PDBs: 8dqv
Q-score: 0.857
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ Pubmed: 36890228 DOI: doi:10.1038/s41586-023-05781-7 ]
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis)
- Nickel (iii) ion (58 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Water (18 Da, Ligand)
- Hydrogenase-2, small subunit (35 kDa, Protein from Mycolicibacterium smegmatis)
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis)
- Oxygen atom (15 Da, Ligand)
- Menadione (172 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6xgq
Q-score: 0.488
Hardy JM, Dunstan RA, Grinter R, Belousoff MJ, Wang J, Pickard D, Venugopal H, Dougan G, Lithgow T, Coulibaly F
Nat Commun (2020) 11 pp. 3748-3748 [ Pubmed: 32719311 DOI: doi:10.1038/s41467-020-17505-w ]
- Bacteriophage sp. (22 MDa, Virus from Bacteriophage sp.)
- Ysd1_17 (39 kDa, Protein from Bacteriophage sp.)
- Ysd1_16 (14 kDa, Protein from Bacteriophage sp.)
Resolution: 3.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 6xgr
Q-score: 0.493
Hardy JM, Dunstan RA, Grinter R, Belousoff MJ, Wang J, Pickard D, Venugopal H, Dougan G, Lithgow T, Coulibaly F
Nat Commun (2020) 11 pp. 3748-3748 [ Pubmed: 32719311 DOI: doi:10.1038/s41467-020-17505-w ]
- Bacteriophage sp. (56 MDa, Virus from Bacteriophage sp.)
- Ysd1_22 major tail protein (40 kDa, Protein from Bacteriophage sp.)