Escherichia coli RNA polymerase unwinding intermediate (I1a) at the lambda PR promoter
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8to1
Q-score: 0.477
Darst SA, Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B
Nat Struct Mol Biol (2024) [ DOI: doi:0.1038/s41594-024-01349-9 ]
- (3r,5s,7r,8r,9s,10s,12s,13r,14s,17r)-10,13-dimethyl-17-[(2r)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1h-cyclopenta[a]phenanthrene-3,7,12-triol (378 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase unwinding intermediate (i1a) at the lambda pr promoter (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
Escherichia coli RNA polymerase unwinding intermediate (I1d) at the lambda PR promoter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8to6
Q-score: 0.465
Darst SA, Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B
Nat Struct Mol Biol (2024) [ DOI: doi:0.1038/s41594-024-01349-9 ]
- (3r,5s,7r,8r,9s,10s,12s,13r,14s,17r)-10,13-dimethyl-17-[(2r)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1h-cyclopenta[a]phenanthrene-3,7,12-triol (378 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Escherichia coli rna polymerase unwinding intermediate (i1d) at the lambda pr promoter (Complex from Escherichia coli)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
Escherichia coli RNA polymerase unwinding intermediate (I1b) at the lambda PR promoter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8to8
Q-score: 0.461
Darst SA, Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B
Nat Struct Mol Biol (2024) [ DOI: doi:0.1038/s41594-024-01349-9 ]
- (3r,5s,7r,8r,9s,10s,12s,13r,14s,17r)-10,13-dimethyl-17-[(2r)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1h-cyclopenta[a]phenanthrene-3,7,12-triol (378 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Escherichia coli rna polymerase unwinding intermediate (i1b) at the lambda pr promoter (Complex from Escherichia coli)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
Escherichia coli RNA polymerase unwinding intermediate (I1c) at the lambda PR promoter
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8toe
Q-score: 0.462
Darst SA, Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B
Nat Struct Mol Biol (2024) [ DOI: doi:0.1038/s41594-024-01349-9 ]
- Escherichia coli rna polymerase unwinding intermediate (i1c) at the lambda pr promoter (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Template strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (32 kDa, DNA from Escherichia phage Lambda)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
Escherichia coli RNA polymerase closed complex intermediate at the lambda PR promoter
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8tom
Q-score: 0.253
Darst SA, Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B
Nat Struct Mol Biol (2024) [ DOI: doi:0.1038/s41594-024-01349-9 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase closed complex intermediate at the lambda pr promoter (Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Template strand of lamdba pr promoter dna (27 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Chapso (631 Da, Ligand)
- Nontemplate strand of lamdba pr promoter dna (27 kDa, DNA from Escherichia phage Lambda)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
Peng R, Fu X, Mendez JH, Randolph PS, Bammes BE, Stagg SM
J Struct Biol X (2022) 7 [ Pubmed: 36578473 DOI: 10.1016/j.yjsbx.2022.100080 ]
Image sets:
Peng R, Fu X, Mendez JH, Randolph PS, Bammes BE, Stagg SM
J Struct Biol X (2022) 7 [ Pubmed: 36578473 DOI: 10.1016/j.yjsbx.2022.100080 ]
Image sets:
Peng R, Fu X, Mendez JH, Randolph PS, Bammes BE, Stagg SM
J Struct Biol X (2022) 7 [ Pubmed: 36578473 DOI: 10.1016/j.yjsbx.2022.100080 ]
Image sets:
Rabbit muscle aldolase determined using single-particle cryo-EM with Apollo camera.
Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8ehg
Q-score: 0.699
Peng R, Fu X, Mendez JH, Randolph PS, Bammes BE, Stagg SM
J Struct Biol X (2023) 7 pp. 100080-100080 [ DOI: doi:10.1016/j.yjsbx.2022.100080 Pubmed: 36578473 ]
- Fructose-bisphosphate aldolase a (39 kDa, Protein from Oryctolagus cuniculus)
- Aldolase from rabbit muscle (14 GDa, Complex from Oryctolagus cuniculus)
Mouse apoferritin heavy chain with zinc determined using single-particle cryo-EM with Apollo camera.
Resolution: 1.66 Å
EM Method: Single-particle
Fitted PDBs: 8emq
Q-score: 0.857
Peng R, Fu X, Mendez JH, Randolph PS, Bammes BE, Stagg SM
J Struct Biol X (2023) 7 pp. 100080-100080 [ Pubmed: 36578473 DOI: doi:10.1016/j.yjsbx.2022.100080 ]
- Water (18 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Ferritin heavy chain, n-terminally processed (20 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- Mouse apoferritin heavy chain (506 kDa, Complex from Mus musculus)