Cryo-EM structure of Acanthamoeba polyphaga mimivirus Fanzor2 ternary complex
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 9b0l
Q-score: 0.475
Schargel RD, Qayyum MZ, Tanwar AS, Kalathur RC, Kellogg EH
Nat Struct Mol Biol (2024) [ Pubmed: 39354233 DOI: doi:10.1038/s41594-024-01394-4 ]
- Dna (5'-d(p*cp*cp*cp*a)-3') (1 kDa, DNA from Acanthamoeba polyphaga mimivirus)
- Dna (5'-d(p*ap*gp*gp*ap*gp*gp*tp*gp*gp*cp*tp*gp*cp*cp*cp*cp*gp*ap*cp*cp*gp*tp*c)-3') (7 kDa, DNA from Acanthamoeba polyphaga mimivirus)
- Acanthamoeba polyphaga mimivirus fanzor2 ternary complex (Complex from Acanthamoeba polyphaga mimivirus)
- Magnesium ion (24 Da, Ligand)
- Tnpb-like protein l79 (60 kDa, Protein from Acanthamoeba polyphaga mimivirus)
- Rna (117-mer) (79 kDa, RNA from Acanthamoeba polyphaga mimivirus)
- Zinc ion (65 Da, Ligand)
- Dna (5'-d(p*gp*ap*cp*gp*gp*tp*cp*gp*gp*gp*c)-3') (3 kDa, DNA from Acanthamoeba polyphaga mimivirus)
Resolution: 2.61 Å
EM Method: Single-particle
Fitted PDBs: 8ur3
Q-score: 0.52
Radka CD, Grace CR, Hasdemir HS, Li Y, Rodriguez CC, Rodrigues P, Oldham ML, Qayyum MZ, Pitre A, MacCain WJ, Kalathur RC, Tajkhorshid E, Rock CO
J Biol Chem (2024) 300 pp. 105627-105627 [ DOI: doi:10.1016/j.jbc.2024.105627 Pubmed: 38211817 ]
- Homodimer of ohya (139 kDa, Complex from Staphylococcus aureus)
- Oleate hydratase (69 kDa, Protein from Staphylococcus aureus)
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 8ur6
Q-score: 0.457
Radka CD, Grace CR, Hasdemir HS, Li Y, Rodriguez CC, Rodrigues P, Oldham ML, Qayyum MZ, Pitre A, MacCain WJ, Kalathur RC, Tajkhorshid E, Rock CO
J Biol Chem (2024) 300 pp. 105627-105627 [ DOI: doi:10.1016/j.jbc.2024.105627 Pubmed: 38211817 ]
- Homodimer of ohya (139 kDa, Complex from Staphylococcus aureus)
- Oleate hydratase (69 kDa, Protein from Staphylococcus aureus)
Cyanobacterial RNA polymerase elongation complex with NusG and CTP
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8urw
Q-score: 0.515
Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS
PNAS (2024) 121 pp. e2311480121-e2311480121 [ Pubmed: 38354263 DOI: doi:10.1073/pnas.2311480121 ]
- Dna-directed rna polymerase subunit alpha (33 kDa, Protein from Synechococcus elongatus)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Cyanobacterial rna polymerase elongation complex with nusg and ctp (Complex from Synechococcus elongatus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechococcus elongatus)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechococcus elongatus)
- Cytidine-5'-triphosphate (483 Da, Ligand)
- Rna (5'-r(p*ap*ap*ap*gp*ap*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (6 kDa, RNA from synthetic construct)
- Transcription termination/antitermination protein nusg (23 kDa, Protein from Synechococcus elongatus)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechococcus elongatus)
- Dna-directed rna polymerase subunit beta' (144 kDa, Protein from Synechococcus elongatus)
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8syi
Q-score: 0.491
Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS
PNAS (2024) 121 pp. e2311480121-e2311480121 [ Pubmed: 38354263 DOI: doi:10.1073/pnas.2311480121 ]
- Dna-directed rna polymerase subunit alpha (33 kDa, Protein from Synechococcus elongatus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechococcus elongatus)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechococcus elongatus)
- Cyrnap-elongation complex (Complex from Synechococcus elongatus)
- Rna (5'-r(p*up*up*cp*ap*ap*ap*gp*cp*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (6 kDa, RNA from synthetic construct)
- Transcription termination/antitermination protein nusg (23 kDa, Protein from Synechococcus elongatus)
- Dna (37-mer) (12 kDa, DNA from synthetic construct)
- Dna (37-mer) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechococcus elongatus)
- Dna-directed rna polymerase subunit beta' (144 kDa, Protein from Synechococcus elongatus)
Escherichia coli RNA polymerase core enzyme
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 7mkp
Q-score: 0.335
Qayyum MZ, Molodtsov V, Renda A, Murakami KS
J Biol Chem (2021) 297 pp. 101404-101404 [ Pubmed: 34774797 DOI: doi:10.1016/j.jbc.2021.101404 ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase core enzyme (Complex from Escherichia coli K-12)
Escherichia coli RNA polymerase and RapA elongation complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7mkn
Q-score: 0.353
Qayyum MZ, Molodtsov V, Renda A, Murakami KS
J Biol Chem (2021) 297 pp. 101404-101404 [ Pubmed: 34774797 DOI: doi:10.1016/j.jbc.2021.101404 ]
- Escherichia coli rna polymerase and rapa elongation complex (Complex from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase-associated protein rapa (109 kDa, Protein from Escherichia coli (strain K12))
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine (481 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli K-12)
- Rna (20-mer) (3 kDa, RNA from Escherichia coli K-12)
Escherichia coli RNA polymerase elongation complex
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 7mko
Q-score: 0.433
Qayyum MZ, Molodtsov V, Renda A, Murakami KS
J Biol Chem (2021) 297 pp. 101404-101404 [ Pubmed: 34774797 DOI: doi:10.1016/j.jbc.2021.101404 ]
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase elongation complex (Complex from Escherichia coli K-12)
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine (481 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli K-12)
- Rna (20-mer) (3 kDa, RNA from Escherichia coli K-12)
Escherichia coli RNA polymerase and RapA binary complex
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 7mkq
Q-score: 0.254
Qayyum MZ, Molodtsov V, Renda A, Murakami KS
J Biol Chem (2021) 297 pp. 101404-101404 [ Pubmed: 34774797 DOI: doi:10.1016/j.jbc.2021.101404 ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (26 kDa, Protein from Escherichia coli (strain K12))
- Escherichia coli rna polymerase and rapa binary complex (Complex from Escherichia coli K-12)
- Rna polymerase-associated protein rapa (109 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
Cryo-EM structure of E. coli RNAP sigma70 holoenzyme
Resolution: 4.25 Å
EM Method: Single-particle
Fitted PDBs: 6c9y
Q-score: -0.016
Narayanan A, Vago FS, Li K, Qayyum MZ, Yernool D, Jiang W, Murakami KS
J Biol Chem (2018) 293 pp. 7367-7375 [ DOI: doi:10.1074/jbc.RA118.002161 Pubmed: 29581236 ]
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli (strain K12))