60 Degree Tilted Single-Particle CryoEM Reconstruction of RNA polymerase
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8txo
Q-score: 0.418
Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Dordevic-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D
Nat Commun (2024) 15 pp. 389-389 [ DOI: doi:10.1038/s41467-023-44555-7 Pubmed: 38195598 ]
- [[(2~{r},3~{s},4~{r},5~{r})-5-(4-azanyl-2-oxidanylidene-1$l^{4},3,5,7-tetrazabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (524 Da, Ligand)
- Rna oligomer (2 kDa, RNA from synthetic construct)
- E. coli rnap transcription elongation complex bound the unnatural dz-ptp base pair in the active site (500 kDa, Complex from Escherichia coli)
- Template single stranded dna (6 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Non-template single stranded dna (5 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8sy5
Q-score: 0.552
Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D
Nat Commun (2023) 14 pp. 8219-8219 [ DOI: doi:10.1038/s41467-023-43735-9 Pubmed: 38086811 ]
- Water (18 Da, Ligand)
- Rna oligomer (2 kDa, RNA from synthetic construct)
- 2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate) (523 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Template single stranded dna (8 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Non-template single stranded dna (5 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- E. coli rnap transcription elongation complex bound the unnatural ds-btp base pair in the active site (500 kDa, Complex from Escherichia coli)
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 8sy6
Q-score: 0.449
Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D
Nat Commun (2023) 14 pp. 8219-8219 [ DOI: doi:10.1038/s41467-023-43735-9 Pubmed: 38086811 ]
- Template single stranded dna (8 kDa, DNA from synthetic construct)
- Rna oligomer (2 kDa, RNA from synthetic construct)
- E. coli rnap transcription elongation complex bound the unnatural db-utp base pair in the active site (500 kDa, Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Uridine 5'-triphosphate (484 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Non-template single stranded dna (5 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- 2'-deoxyguanosine-5'-monophosphate (347 Da, Ligand)
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8sy7
Q-score: 0.522
Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D
Nat Commun (2023) 14 pp. 8219-8219 [ DOI: doi:10.1038/s41467-023-43735-9 Pubmed: 38086811 ]
- Water (18 Da, Ligand)
- Template single stranded dna (8 kDa, DNA from synthetic construct)
- Rna oligomer (2 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- E. coli rnap transcription elongation complex bound the unnatural db-stp base pair in the active site (500 kDa, Complex from Escherichia coli)
- Non-template single stranded dna (5 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- [[(2~{r},3~{s},4~{r},5~{s})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (497 Da, Ligand)