Structure of NaCT-PF4a complex
Resolution: 2.13 Å
EM Method: Single-particle
Fitted PDBs: 8uvb
Q-score: 0.618
Li Y, Song J, Mikusevic V, Marden JJ, Becerril A, Kuang H, Wang B, Rice WJ, Mindell JA, Wang DN
Nat Struct Mol Biol (2024) [ Pubmed: 39622972 DOI: doi:10.1038/s41594-024-01433-0 ]
- (2r)-2-hydroxy-2-[2-(2-methoxy-5-methylpyridin-3-yl)ethyl]butanedioic acid (283 Da, Ligand)
- Dimer of nact in complex with pf4a (63 kDa, Complex from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- Solute carrier family 13 member 5 (63 kDa, Protein from Homo sapiens)
Structure of NaDC3-aKG complex
Resolution: 2.09 Å
EM Method: Single-particle
Fitted PDBs: 8uvc
Q-score: 0.638
Li Y, Song J, Mikusevic V, Marden JJ, Becerril A, Kuang H, Wang B, Rice WJ, Mindell JA, Wang DN
Nat Struct Mol Biol (2024) [ Pubmed: 39622972 DOI: doi:10.1038/s41594-024-01433-0 ]
- Tetradecane (198 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 2-oxoglutaric acid (146 Da, Ligand)
- Na(+)/dicarboxylate cotransporter 3 (67 kDa, Protein from Homo sapiens)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Dimer of nadc3 in complex with alpha-ketoglutarate (63 kDa, Complex from Homo sapiens)
Structure of NaDC3-PF4a complex
Resolution: 2.16 Å
EM Method: Single-particle
Fitted PDBs: 8uvd
Q-score: 0.625
Li Y, Song J, Mikusevic V, Marden JJ, Becerril A, Kuang H, Wang B, Rice WJ, Mindell JA, Wang DN
Nat Struct Mol Biol (2024) [ Pubmed: 39622972 DOI: doi:10.1038/s41594-024-01433-0 ]
- Tetradecane (198 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Na(+)/dicarboxylate cotransporter 3 (67 kDa, Protein from Homo sapiens)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Dimer of nadc3 in complex with pf4a (63 kDa, Complex from Homo sapiens)
- (2r)-2-hydroxy-2-[2-(2-methoxy-5-methylpyridin-3-yl)ethyl]butanedioic acid (283 Da, Ligand)
Structure of NaDC3-Succinate complex in Coo-Ci conformation
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8uve
Q-score: 0.551
Li Y, Song J, Mikusevic V, Marden JJ, Becerril A, Kuang H, Wang B, Rice WJ, Mindell JA, Wang DN
Nat Struct Mol Biol (2024) [ Pubmed: 39622972 DOI: doi:10.1038/s41594-024-01433-0 ]
- Tetradecane (198 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Succinic acid (118 Da, Ligand)
- Na(+)/dicarboxylate cotransporter 3 (67 kDa, Protein from Homo sapiens)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Dimer of nadc3 in complex with succinate (63 kDa, Complex from Homo sapiens)
Structure of NaDC3-DMS complex in Ci-Ci conformation
Resolution: 2.17 Å
EM Method: Single-particle
Fitted PDBs: 8uvf
Q-score: 0.635
Li Y, Song J, Mikusevic V, Marden JJ, Becerril A, Kuang H, Wang B, Rice WJ, Mindell JA, Wang DN
Nat Struct Mol Biol (2024) [ Pubmed: 39622972 DOI: doi:10.1038/s41594-024-01433-0 ]
- Tetradecane (198 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Na(+)/dicarboxylate cotransporter 3 (67 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Dimer of nadc3 in complex with 2,3-dms (63 kDa, Complex from Homo sapiens)
Structure of NaDC3-DMS complex in Co-Ci conformation
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8uvg
Q-score: 0.517
Li Y, Song J, Mikusevic V, Marden JJ, Becerril A, Kuang H, Wang B, Rice WJ, Mindell JA, Wang DN
Nat Struct Mol Biol (2024) [ Pubmed: 39622972 DOI: doi:10.1038/s41594-024-01433-0 ]
- Tetradecane (198 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Na(+)/dicarboxylate cotransporter 3 (67 kDa, Protein from Homo sapiens)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- (2r,3s)-2,3-dimethylbutanedioic acid (146 Da, Ligand)
- Dimer of nadc3 in complex with 2,3-dms (63 kDa, Complex from Homo sapiens)
Structure of NaCT-succ complex
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 8uvh
Q-score: 0.57
Li Y, Song J, Mikusevic V, Marden JJ, Becerril A, Kuang H, Wang B, Rice WJ, Mindell JA, Wang DN
Nat Struct Mol Biol (2024) [ Pubmed: 39622972 DOI: doi:10.1038/s41594-024-01433-0 ]
- Solute carrier family 13 member 5 (63 kDa, Protein from Homo sapiens)
- Dimer of nact complex in succinate (63 kDa, Complex from Homo sapiens)
Structure of NaDC3-Succinate complex in Coo-Coo conformation
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8uvi
Q-score: 0.548
Li Y, Song J, Mikusevic V, Marden JJ, Becerril A, Kuang H, Wang B, Rice WJ, Mindell JA, Wang DN
Nat Struct Mol Biol (2024) [ Pubmed: 39622972 DOI: doi:10.1038/s41594-024-01433-0 ]
- Tetradecane (198 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Succinic acid (118 Da, Ligand)
- Na(+)/dicarboxylate cotransporter 3 (67 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Dimer of nadc3 in complex with succinate (63 kDa, Complex from Homo sapiens)
Cryo-EM structure of the active Lactococcus lactis Csm bound to target in post-cleavage stage
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 9ash
Q-score: 0.56
Goswami HN, Ahmadizadeh F, Wang B, Addo-Yobo D, Zhao Y, Whittington AC, He H, Terns MP, Li H
Nucleic Acids Res (2024) 52 pp. 10619-10629 [ DOI: doi:10.1093/nar/gkae603 Pubmed: 38989619 ]
- Crispr system cms protein csm5 (40 kDa, Protein from Lactococcus lactis subsp. lactis)
- Target rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Atp bound lactococcus lactis csm crispr-cas complex with stable cas10 (Complex from Lactococcus lactis subsp. lactis)
- Water (18 Da, Ligand)
- Rna (5'-d(*(atp))-r(p*ap*a)-3') (1 kDa, RNA from Lactococcus lactis subsp. lactis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated protein csm4 (33 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr system cms endoribonuclease csm3 (23 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr system cms protein csm2 (17 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Crispr system single-strand-specific deoxyribonuclease cas10/csm1 (subtype iii-a) (87 kDa, Protein from Lactococcus lactis subsp. lactis)
Cryo-EM structure of the active Lactococcus lactis Csm bound to target in pre-cleavage stage
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 9asi
Q-score: 0.467
Goswami HN, Ahmadizadeh F, Wang B, Addo-Yobo D, Zhao Y, Whittington AC, He H, Terns MP, Li H
Nucleic Acids Res (2024) 52 pp. 10619-10629 [ DOI: doi:10.1093/nar/gkae603 Pubmed: 38989619 ]
- Crispr system cms protein csm5 (40 kDa, Protein from Lactococcus lactis subsp. lactis)
- Target rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated protein csm4 (33 kDa, Protein from Lactococcus lactis subsp. lactis)
- Adenosine monophosphate (347 Da, Ligand)
- Crispr system cms endoribonuclease csm3 (23 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr system cms protein csm2 (17 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr system single-strand-specific deoxyribonuclease cas10/csm1 (subtype iii-a) (87 kDa, Protein from Lactococcus lactis subsp. lactis)
- Crispr rna (11 kDa, RNA from Lactococcus lactis subsp. lactis)
- Lactococcus lactis csm crispr-cas complex, atp bound and cas10 flexible (Complex from Lactococcus lactis subsp. lactis)