Structure of Gabija AB complex
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8tjy
Q-score: 0.534
Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01283-w Pubmed: 38627580 ]
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus)
- Gabija protein gajb (57 kDa, Protein from Bacillus cereus)
- Tetramer of gabija protein a (Complex from Bacillus cereus)
Structure of Gabija AB complex
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8tk0
Q-score: 0.496
Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01283-w Pubmed: 38627580 ]
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus)
- Tetramer of gabija protein a (Complex from Bacillus cereus)
Structure of Gabija AB complex 1
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8tk1
Q-score: 0.453
Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01283-w Pubmed: 38627580 ]
- Tetramer of gabija protein ab (4:4) (Complex from Bacillus cereus)
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus)
- Gabija protein gajb (57 kDa, Protein from Bacillus cereus)
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 ]
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Sir2-like domain-containing protein (46 kDa, Protein from Escherichia coli)
- E. coli sir2-hera complex (Complex 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)
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)
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Sir2-like domain-containing protein (46 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)
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 ]
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Sir2-hera complex 2(12:5) (Complex from Escherichia coli)
- Sir2-like domain-containing protein (46 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)
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 ]
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Sir2_hera complex (12:6) with atpgamas (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Sir2-like domain-containing protein (46 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)
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 ]
- Nucleoside triphosphate hydrolase (68 kDa, Protein from Escherichia coli)
- Hera-sir2 complex bound with nad+ (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Sir2-like domain-containing protein (46 kDa, Protein from Escherichia coli)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- [(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)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7y6l
Q-score: 0.492
Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Lin Q, Sakuma M, Kawahara E, Yamazaki I, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Hisano T, Moriyama S, Takahashi Y, Ito M, Imai M, Maemura T, Furusawa Y, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T
iScience (2023) 26 pp. 106955-106955 [ DOI: doi:10.1016/j.isci.2023.106955 Pubmed: 37288342 ]
- The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab816 (560 kDa, Complex from Homo sapiens)
- Ab816 heavy chain (28 kDa, Protein from Homo sapiens)
- Ab816 light chain (26 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)