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 ]
- Cu(i)-s-mo(iv)(=o)oh cluster (224 Da, Ligand)
- Water (18 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Carbon monoxide dehydrogenase (large chain), coxl (85 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Pterin cytosine dinucleotide (696 Da, Ligand)
- [2fe-2s] binding domain protein (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Carbon monoxide dehydrogenase medium chain (31 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mocu carbon monoxide dehydrogenase (mocu-codh) (270 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Flavin-adenine dinucleotide (785 Da, Ligand)
Ubiquitin transfer from E2 to E3: UBE2D2-ubiquitin linked to HECT E3 ligase UBR5
Hehl LA, Horn-Ghetko D, Prabu JR, Vollrath R, Vu DT, Perez Berrocal DA, Mulder MPC, van der Heden van Noort GJ, Schulman BA
Nat Chem Biol (2024) 20 pp. 190-200 [ DOI: doi:10.1038/s41589-023-01414-2 Pubmed: 37620400 ]
- Ub (Complex from Homo sapiens)
- Dimeric ubr5 crosslinked to ube2d2~ub (9 kDa, Complex from Homo sapiens)
- Ube2d2 (Complex from Homo sapiens)
Cryo-EM Structure of Bl_Man38A at 2.7 A
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7ufr
Q-score: 0.602
Santos CR, Cordeiro RL, Domingues MN, Borges AC, de Farias MA, Van Heel M, Murakami MT, Portugal RV
Nat Chem Biol (2022) [ ]
- Tetramer of bl_man38a (471 kDa, Complex from Bifidobacterium longum)
- Zinc ion (65 Da, Ligand)
- Alpha-mannosidase (117 kDa, Protein from Bifidobacterium longum)
Cryo-EM Structure of Bl_Man38B at 3.4 A
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ufs
Q-score: 0.486
Santos CR, Cordeiro RL, Domingues MN, Borges AC, de Farias MA, Van Heel M, Murakami MT, Portugal RV
Nat Chem Biol (2022) [ ]
- Alpha-mannosidase (118 kDa, Protein from Bifidobacterium longum)
- Zinc ion (65 Da, Ligand)
- Tetramer of bl_man38b (475 kDa, Complex from Bifidobacterium longum)
Cryo-EM Structure of Bl_Man38C at 2.9 A
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7uft
Q-score: 0.574
Santos CR, Cordeiro RL, Domingues MN, Borges AC, de Farias MA, Van Heel M, Murakami MT, Portugal RV
Nat Chem Biol (2022) [ ]
- Alpha-mannosidase (117 kDa, Protein from Bifidobacterium longum)
- Tetramer of bl_man38c (470 kDa, Complex from Bifidobacterium longum)
- Zinc ion (65 Da, Ligand)
Cryo-EM Structure of Bl_Man38A nucleophile mutant in complex with mannose at 2.7 A
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7ufu
Q-score: 0.563
Santos CR, Cordeiro RL, Domingues MN, Borges AC, de Farias MA, Van Heel M, Murakami MT, Portugal RV
Nat Chem Biol (2022) [ ]
- Zinc ion (65 Da, Ligand)
- Alpha-mannosidase (117 kDa, Protein from Bifidobacterium longum)
- Alpha-d-mannopyranose (180 Da, Ligand)
- Tetramer of nucleophile mutant version of bl1_man38a in complex with mannose (471 kDa, Complex from Bifidobacterium longum)
Structure of RyR1 (Ca2+/Caffeine/ATP/CaM1234/CHL)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6m2w
Q-score: 0.309
Ma R, Haji-Ghassemi O, Ma D, Jiang H, Lin L, Yao L, Samurkas A, Li Y, Wang Y, Cao P, Wu S, Zhang Y, Murayama T, Moussian B, Van Petegem F, Yuchi Z
Nat Chem Biol (2020) 16 pp. 1246-1254 [ Pubmed: 32807966 DOI: doi:10.1038/s41589-020-0627-5 ]
- 5-bromanyl-n-[4-chloranyl-2-methyl-6-(methylcarbamoyl)phenyl]-2-(3-chloranylpyridin-2-yl)pyrazole-3-carboxamide (483 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Calmodulin-1 (16 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Ryr1 (Complex from Oryctolagus cuniculus)
- Caffeine (194 Da, Ligand)
- Fkbp12.6 and cam1234 (Complex from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Ryr1 ca2 /atp/caffeine/cam1234/chl (2 MDa, Complex)
- Ryanodine receptor 1,ryanodine receptor 1,ryanodine receptor 1,ryanodine receptor 1,ryanodine receptor 1,ryanodine receptor 1,ryanodine receptor 1 (539 kDa, Protein from Oryctolagus cuniculus)
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 7cf9
Q-score: 0.232
Ma R, Haji-Ghassemi O, Ma D, Jiang H, Lin L, Yao L, Samurkas A, Li Y, Wang Y, Cao P, Wu S, Zhang Y, Murayama T, Moussian B, Van Petegem F, Yuchi Z
Nat Chem Biol (2020) 16 pp. 1246-1254 [ Pubmed: 32807966 DOI: doi:10.1038/s41589-020-0627-5 ]
- Ryanodine receptor 1,ryr1 (539 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- 5-bromanyl-n-[4-chloranyl-2-methyl-6-(methylcarbamoyl)phenyl]-2-(3-chloranylpyridin-2-yl)pyrazole-3-carboxamide (483 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Ryr1 (Complex from Oryctolagus cuniculus)
- Fkbp1b (Complex from Homo sapiens)
- Ryr1 ca2+/chl (2 MDa, Complex)