E. coli RNA polymerase paused at ops site
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8pdy
Q-score: 0.409
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna and rna (Complex from Escherichia coli)
- Non-template dna (35-mer) (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation complex paused at ops site, assembled on fully complementary nucleic acid scaffold (399 kDa, Complex)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Template dna (35-mer) (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Rna (5'-r(p*up*gp*gp*cp*gp*gp*up*ap*gp*cp*gp*u)-3') (5 kDa, RNA from Escherichia coli)
Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 deleted strain
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 6skg
Q-score: 0.614
Sas-Chen A, Thomas JM, Matzov D, Taoka M, Nance KD, Nir R, Bryson KM, Shachar R, Liman GLS, Burkhart BW, Gamage ST, Nobe Y, Briney CA, Levy MJ, Fuchs RT, Robb GB, Hartmann J, Sharma S, Lin Q, Florens L, Washburn MP, Isobe T, Santangelo TJ, Shalev-Benami M, Meier JL, Schwartz S
Nature (2020) 583 pp. 638-643 [ DOI: doi:10.1038/s41586-020-2418-2 Pubmed: 32555463 ]
- 50s ribosomal protein l21e (11 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s17 (13 kDa, Protein from Thermococcus kodakarensis)
- Unknown ribosomal protein (2 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s8e (14 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s9 (15 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s17e (8 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s14 type z (6 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l14e (8 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s28e (7 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s8 (14 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l6 (20 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s2 (23 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s5 (26 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s19e (17 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l15e (22 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l29 (7 kDa, Protein from Thermococcus kodakarensis)
- Lsu ribosomal protein l41e (5 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l34e (10 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s3ae (23 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l37e (7 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l37ae (9 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l18ae (9 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s3 (23 kDa, Protein from Thermococcus kodakarensis)
- 16s ribosomal rna (487 kDa, RNA from Thermococcus kodakarensis)
- 30s ribosomal protein s7 (24 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l10e (21 kDa, Protein from Thermococcus kodakarensis)
- Ribosomal protein el35a (11 kDa, Protein from Thermococcus kodakarensis)
- Predicted exosome subunit, upf0023 family (26 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l24e (8 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s24e (11 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l3 (39 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s27e (7 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l5 (21 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s15 (17 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l24 (14 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l2 (26 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l39e (6 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l30e (10 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l14 (15 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s4 (21 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s11 (15 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s19 (15 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l4 (28 kDa, Protein from Thermococcus kodakarensis)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l23 (9 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l31e (10 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s4e (27 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s10 (11 kDa, Protein from Thermococcus kodakarensis)
- Predicted zinc-ribbon rna-binding protein involved in translation (7 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l7ae (13 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l18 (22 kDa, Protein from Thermococcus kodakarensis)
- 30s ribosomal protein s6e (13 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l15 (16 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l18e (13 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l22 (17 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l40e (5 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l44e (11 kDa, Protein from Thermococcus kodakarensis)
- Water (18 Da, Ligand)
- 50s ribosomal protein l13 (16 kDa, Protein from Thermococcus kodakarensis)
- 23s ribosomal rna (987 kDa, RNA from Thermococcus kodakarensis)
- 30s ribosomal protein s13 (17 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l19e (17 kDa, Protein from Thermococcus kodakarensis)
- Nucleic acid-binding protein, containing c2h2 zinc-finger (5 kDa, Protein from Thermococcus kodakarensis)
- 70s ribosome from thermococcus kodakarensis (Complex from Thermococcus kodakarensis)
- 30s ribosomal protein s12 (16 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l32e (14 kDa, Protein from Thermococcus kodakarensis)
- 50s ribosomal protein l30 (17 kDa, Protein from Thermococcus kodakarensis)
- 5s ribosomal rna (40 kDa, RNA from Thermococcus kodakarensis)
RNA Polymerase I Closed Conformation 2 (CC2)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6rql
Q-score: 0.355
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW
Nat Commun (2019) 10 pp. 5543-5543 [ Pubmed: 31804486 DOI: doi:10.1038/s41467-019-13510-w ]
- Dna-directed rna polymerase i subunit rpa34 (26 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Template strand (21 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa190 (186 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn11 (59 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor (Complex from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn7 (60 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i closed complex conformation 2 (cc2) (Complex)
- Dna-directed rna polymerase i subunit rpa135 (135 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa43 (36 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate strand (21 kDa, DNA from synthetic construct)
- Rna polymerase i (Complex from Saccharomyces cerevisiae)
- Nucleic acid (Complex from synthetic construct)
- Rna polymerase i-specific transcription initiation factor rrn3 (72 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa14 (14 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn6 (102 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa49 (46 kDa, Protein from Saccharomyces cerevisiae)