Wakabayashi T, Oide M, Matsui Y, Nakasako M
To Be Published
- Ammonium ion (18 Da, Ligand)
- Glutamate dehydrogenase (46 kDa, Protein from Thermococcus profundus)
- 2-oxoglutaric acid (146 Da, Ligand)
- Water (18 Da, Ligand)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Hexamer of w89f mutated glutamate dehydrogenase (280 kDa, Cellular component from Thermococcus profundus)
Resolution: 2.63 Å
EM Method: Single-particle
Fitted PDBs: 8xcs
Q-score: 0.638
Wakabayashi T, Oide M, Nakasako M
Sci Rep (2024) 14 pp. 11165-11165 [ Pubmed: 38750092 DOI: doi:10.1038/s41598-024-61793-x ]
- Water (18 Da, Ligand)
- Glutamate dehydrogenase (46 kDa, Protein from Thermococcus profundus)
- Ammonium ion (18 Da, Ligand)
- Hexamer of glutamate dehydrogenase in the presence of nadp and glutamate (280 kDa, Complex from Thermococcus profundus)
- 2-oxoglutaric acid (146 Da, Ligand)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8xd6
Q-score: 0.626
Wakabayashi T, Oide M, Nakasako M
Sci Rep (2024) 14 pp. 11165-11165 [ Pubmed: 38750092 DOI: doi:10.1038/s41598-024-61793-x ]
- Water (18 Da, Ligand)
- Glutamate dehydrogenase (46 kDa, Protein from Thermococcus profundus)
- Ammonium ion (18 Da, Ligand)
- Hexamer of glutamate dehydrogenase in the presence of nadp and glutamate (280 kDa, Complex from Thermococcus profundus)
- 2-oxoglutaric acid (146 Da, Ligand)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
Structure of a group II intron ribonucleoprotein in the pre-ligation (pre-2F) state
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8t2r
Q-score: 0.459
Nature (2023) 624 pp. 682-688 [ DOI: doi:10.1038/s41586-023-06746-6 Pubmed: 37993708 ]
- Ammonium ion (18 Da, Ligand)
- Intron rnp complex in pre-2f (300 kDa, Complex from [Eubacterium] rectale)
- 5'exon (2 kDa, RNA from [Eubacterium] rectale)
- Intron (208 kDa, RNA from [Eubacterium] rectale)
- Calcium ion (40 Da, Ligand)
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
Structure of a group II intron ribonucleoprotein in the pre-branching (pre-1F) state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8t2s
Q-score: 0.48
Nature (2023) 624 pp. 682-688 [ DOI: doi:10.1038/s41586-023-06746-6 Pubmed: 37993708 ]
- Rna (551-mer) (211 kDa, RNA from [Eubacterium] rectale)
- Ammonium ion (18 Da, Ligand)
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
- Intron rnp complex in pre-1f (300 kDa, Complex from [Eubacterium] rectale)
- Calcium ion (40 Da, Ligand)
Structure of a group II intron ribonucleoprotein in the post-ligation (post-2F) state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8t2t
Q-score: -0.023
Nature (2023) 624 pp. 682-688 [ DOI: doi:10.1038/s41586-023-06746-6 Pubmed: 37993708 ]
- Rna (5'-r(p*up*up*up*cp*up*up*up*up*g)-3') (2 kDa, RNA from [Eubacterium] rectale)
- Rna (537-mer) (206 kDa, RNA from [Eubacterium] rectale)
- Magnesium ion (24 Da, Ligand)
- Ammonium ion (18 Da, Ligand)
- Intron rnp complex in post-2f (300 kDa, Complex from [Eubacterium] rectale)
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
CryoEM Structure of an Group II Intron Retroelement (apo-complex)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7uim
Q-score: 0.262
Chung K, Xu L, Chai P, Peng J, Devarkar SC, Pyle AM
Science (2022) 378 pp. 627-634 [ Pubmed: 36356138 DOI: doi:10.1126/science.abq2844 ]
- Ammonium ion (18 Da, Ligand)
- E.r iic intron (206 kDa, RNA from [Eubacterium] rectale)
- Complex of rna and protein (250 kDa, Complex from [Eubacterium] rectale)
- Magnesium ion (24 Da, Ligand)
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
CryoEM Structure of an Group II Intron Retroelement
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7uin
Q-score: 0.467
Chung K, Xu L, Chai P, Peng J, Devarkar SC, Pyle AM
Science (2022) 378 pp. 627-634 [ Pubmed: 36356138 DOI: doi:10.1126/science.abq2844 ]
- Magnesium ion (24 Da, Ligand)
- Ternary complex of rna, protein and dna (260 kDa, Complex from [Eubacterium] rectale)
- Water (18 Da, Ligand)
- Ammonium ion (18 Da, Ligand)
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
- Dna (37-mer) (11 kDa, DNA from [Eubacterium] rectale)
- E.r iic intron (206 kDa, RNA from [Eubacterium] rectale)