Cryo-EM structure of the tetrameric SPARSA gRNA-ssDNA-NAD+ complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8y82
Q-score: 0.412
Cui N, Zhang JT, Li Z, Wei XY, Wang J, Jia N
Nat Commun (2024) 15 pp. 8610-8610 [ Pubmed: 39366953 DOI: doi:10.1038/s41467-024-52910-5 ]
- Rna (21-mer) (6 kDa, RNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
- Tetrameric sparsagrna-ssdna-nad+ complex (Complex from Geobacter sulfurreducens)
- Magnesium ion (24 Da, Ligand)
- Adenosine monophosphate (347 Da, Ligand)
- Dna (25-mer) (7 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
Cryo-EM structure of DSR2 (H171A)-tube-NAD+ complex
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8wyb
Q-score: 0.334
Zhang JT, Liu XY, Li Z, Wei XY, Song XY, Cui N, Zhong J, Li H, Jia N
Nat Commun (2024) 15 pp. 2797-2797 [ DOI: doi:10.1038/s41467-024-47177-9 Pubmed: 38555355 ]
- Bacillus phage spr tube protein (29 kDa, Protein from Bacillus phage SPR)
- Sir2-like domain-containing protein (118 kDa, Protein from Bacillus subtilis)
- Cryoem structure of dsr2 (h171a)-tube-nad+ complex (Complex from Bacillus subtilis)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Cryo-EM structure of DSR2 (H171A)-tube-NAD+ (partial) complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8wyc
Q-score: 0.547
Zhang JT, Liu XY, Li Z, Wei XY, Song XY, Cui N, Zhong J, Li H, Jia N
Nat Commun (2024) 15 pp. 2797-2797 [ DOI: doi:10.1038/s41467-024-47177-9 Pubmed: 38555355 ]
- Cryoem structure of dsr2 (h171a)-tube nad+ (half) complex (Complex from Bacillus subtilis)
- Bacillus phage spr tube protein (29 kDa, Protein from Bacillus phage SPR)
- Sir2-like domain-containing protein (118 kDa, Protein from Bacillus subtilis)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Cryo-EM structure of DSR2-DSAD1-NAD+ (partial) complex
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8wyf
Q-score: 0.546
Zhang JT, Liu XY, Li Z, Wei XY, Song XY, Cui N, Zhong J, Li H, Jia N
Nat Commun (2024) 15 pp. 2797-2797 [ DOI: doi:10.1038/s41467-024-47177-9 Pubmed: 38555355 ]
- Sir2 family protein (118 kDa, Protein from Bacillus subtilis)
- Cryoem structure of dsr2 -dsad1-nad+ (half) complex (Complex from Bacillus subtilis)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Bacillus phage spbeta dsad1 protein (16 kDa, Protein from Bacillus phage SPBc2)
E. coli SIR2-HerA complex (hexamer HerA bound with dodecamer Sir2)
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 8su9
Q-score: 0.562
Shen Z, Lin Q, Yang XY, Fosuah E, Fu TM
Mol Cell (2023) 83 pp. 4586-4599.e5 [ DOI: doi:10.1016/j.molcel.2023.11.007 Pubmed: 38096827 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Sir2-like domain-containing protein (46 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- E. coli sir2-hera complex (Complex from Escherichia coli)
E. coli SIR2-HerA complex (dodecamer SIR2 bound 4 protomers of HerA)
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8suw
Q-score: 0.439
Shen Z, Lin Q, Yang XY, Fosuah E, Fu TM
Mol Cell (2023) 83 pp. 4586-4599.e5 [ DOI: doi:10.1016/j.molcel.2023.11.007 Pubmed: 38096827 ]
- Sir2-hera complex(dodecomaer sir2 bound with four protomers of hera) (Complex from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Sir2-like domain-containing protein (46 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
E. coli SIR2-HerA complex (dodecamer SIR2 pentamer HerA)
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8sub
Q-score: 0.515
Shen Z, Lin Q, Yang XY, Fosuah E, Fu TM
Mol Cell (2023) 83 pp. 4586-4599.e5 [ DOI: doi:10.1016/j.molcel.2023.11.007 Pubmed: 38096827 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Sir2-hera complex 2(12:5) (Complex from Escherichia coli)
- Sir2-like domain-containing protein (46 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8sxx
Q-score: 0.2
Shen Z, Lin Q, Yang XY, Fosuah E, Fu TM
Mol Cell (2023) 83 pp. 4586-4599.e5 [ DOI: doi:10.1016/j.molcel.2023.11.007 Pubmed: 38096827 ]
- E. coli dodecamer sir2 (Complex from Escherichia coli)
- Sir2-like domain-containing protein (46 kDa, Protein from Escherichia coli)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
E. coli Sir2_HerA complex (12:6) with ATPgamaS
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8uae
Q-score: 0.492
Shen Z, Lin Q, Yang XY, Fosuah E, Fu TM
Mol Cell (2023) 83 pp. 4586-4599.e5 [ DOI: doi:10.1016/j.molcel.2023.11.007 Pubmed: 38096827 ]
- Sir2_hera complex (12:6) with atpgamas (Complex from Escherichia coli)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Sir2-like domain-containing protein (46 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
E. coli Sir2_HerA complex (12:6) bound with NAD+
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8uaf
Q-score: 0.393
Shen Z, Lin Q, Yang XY, Fosuah E, Fu TM
Mol Cell (2023) 83 pp. 4586-4599.e5 [ DOI: doi:10.1016/j.molcel.2023.11.007 Pubmed: 38096827 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Sir2-like domain-containing protein (46 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Hera-sir2 complex bound with nad+ (Complex from Escherichia coli)