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 ]
- Acanthamoeba polyphaga mimivirus fanzor2 ternary complex (Complex 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)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*cp*cp*cp*a)-3') (1 kDa, DNA from Acanthamoeba polyphaga mimivirus)
- Rna (117-mer) (79 kDa, RNA from Acanthamoeba polyphaga mimivirus)
- Tnpb-like protein l79 (60 kDa, Protein from Acanthamoeba polyphaga mimivirus)
- Dna (5'-d(p*gp*ap*cp*gp*gp*tp*cp*gp*gp*gp*c)-3') (3 kDa, DNA from Acanthamoeba polyphaga mimivirus)
- Zinc ion (65 Da, Ligand)
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 [ Pubmed: 38211817 DOI: doi:10.1016/j.jbc.2024.105627 ]
- 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 [ Pubmed: 38211817 DOI: doi:10.1016/j.jbc.2024.105627 ]
- 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 [ DOI: doi:10.1073/pnas.2311480121 Pubmed: 38354263 ]
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- 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)
- Dna-directed rna polymerase subunit alpha (33 kDa, Protein from Synechococcus elongatus)
- Transcription termination/antitermination protein nusg (23 kDa, Protein from Synechococcus elongatus)
- Cytidine-5'-triphosphate (483 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (144 kDa, Protein from Synechococcus elongatus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechococcus elongatus)
- Cyanobacterial rna polymerase elongation complex with nusg and ctp (Complex from Synechococcus elongatus)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechococcus elongatus)
- Dna (40-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechococcus elongatus)
- Zinc ion (65 Da, Ligand)
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 [ DOI: doi:10.1073/pnas.2311480121 Pubmed: 38354263 ]
- Dna-directed rna polymerase subunit alpha (33 kDa, Protein from Synechococcus elongatus)
- Transcription termination/antitermination protein nusg (23 kDa, Protein from Synechococcus elongatus)
- Dna (37-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta' (144 kDa, Protein from Synechococcus elongatus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (123 kDa, Protein from Synechococcus elongatus)
- Dna (37-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit gamma (71 kDa, Protein from Synechococcus elongatus)
- Dna-directed rna polymerase subunit omega (8 kDa, Protein from Synechococcus elongatus)
- Cyrnap-elongation complex (Complex from Synechococcus elongatus)
- Zinc ion (65 Da, Ligand)
- 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)
Mycobacterium tuberculosis paused transcription complex with Bacillus subtilis NusG
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8ehq
Q-score: 0.506
Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS
PNAS (2023) 120 pp. e2218516120-e2218516120 [ DOI: doi:10.1073/pnas.2218516120 Pubmed: 36745813 ]
- Paused transcription complex with nusg (Complex from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (38-mer) (12 kDa, DNA from synthetic construct)
- Rna (29-mer) (9 kDa, RNA from synthetic construct)
- Dna (38-mer) (12 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Magnesium ion (24 Da, Ligand)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Zinc ion (65 Da, Ligand)
M. tuberculosis RNAP pause escaped complex with Bacillus subtilis NusG and GMPCPP
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8ej3
Q-score: 0.511
Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS
PNAS (2023) 120 pp. e2218516120-e2218516120 [ DOI: doi:10.1073/pnas.2218516120 Pubmed: 36745813 ]
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (29-mer) (12 kDa, DNA from synthetic construct)
- Rna (5'-r(p*up*cp*gp*gp*cp*ap*gp*gp*ap*gp*ap*gp*gp*up*a)-3') (9 kDa, RNA from synthetic RNA)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Magnesium ion (24 Da, Ligand)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Pause escaped transcription complex with nusg and gmpcpp (Complex from Mycobacterium tuberculosis H37Rv)
- Dna (32-mer) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
Mycobacterium tuberculosis transcription elongation complex with Bacillus subtilis NusG (EC_LG)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8eoe
Q-score: 0.475
Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS
PNAS (2023) 120 pp. e2218516120-e2218516120 [ DOI: doi:10.1073/pnas.2218516120 Pubmed: 36745813 ]
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (38-mer) (12 kDa, DNA from synthetic construct)
- Rna (9 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Magnesium ion (24 Da, Ligand)
- M. tuberculosis transcription elongation complex with nusg (Complex from Mycobacterium tuberculosis H37Rv)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (35-mer) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
Mycobacterium tuberculosis transcription elongation complex with Bacillus subtilis NusG (EC_PG)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8eof
Q-score: 0.467
Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS
PNAS (2023) 120 pp. e2218516120-e2218516120 [ DOI: doi:10.1073/pnas.2218516120 Pubmed: 36745813 ]
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (38-mer) (12 kDa, DNA from synthetic construct)
- Rna (29-mer) (9 kDa, RNA from synthetic RNA)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Magnesium ion (24 Da, Ligand)
- M. tuberculosis transcription elongation complex with nusg (Complex from Mycobacterium tuberculosis H37Rv)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (35-mer) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
M. tuberculosis RNAP elongation complex with NusG and CMPCPP
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8eos
Q-score: 0.502
Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS
PNAS (2023) 120 pp. e2218516120-e2218516120 [ DOI: doi:10.1073/pnas.2218516120 Pubmed: 36745813 ]
- Rna (5'-r(p*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 (25 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine (481 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (38-mer) (12 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation complex with m. tuberculosis nusg and cmpcpp (Complex from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna (36-mer) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)