Methanosarcine mazei tRNAPyl in A-site of ribosome
Krahn N, Zhang J, Melnikov SV, Tharp JM, Villa A, Patel A, Howard RJ, Gabir H, Patel TR, Stetefeld J, Puglisi J, Soll D
Nucleic Acids Res (2024) 52 pp. 513-524 [ Pubmed: 38100361 DOI: doi:10.1093/nar/gkad1188 ]
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 8rd8
Q-score: 0.637
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV
Nature (2024) 626 pp. 1125-1132 [ Pubmed: 38355796 DOI: doi:10.1038/s41586-024-07041-8 ]
- Small ribosomal subunit protein us15 (10 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul22 (11 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us4 (24 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us2 (29 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul23 (12 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Psychrobacter urativorans)
- Magnesium ion (24 Da, Ligand)
- Small ribosomal subunit protein bs18 (8 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us3 (27 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl31b (10 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl25 (23 kDa, Protein from Psychrobacter urativorans)
- Methyl-accepting chemotaxis protein (41 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Psychrobacter urativorans)
- 5s rrna (36 kDa, RNA from Psychrobacter urativorans)
- Large ribosomal subunit protein ul4 (21 kDa, Protein from Psychrobacter urativorans)
- 23s rrna (933 kDa, RNA from Psychrobacter urativorans)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Psychrobacter urativorans)
- Ribosomes isolated from ice-treated cultures of psychrobacter urativorans. (Complex from Psychrobacter urativorans)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl19 (14 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul5 (19 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul13 (15 kDa, Protein from Psychrobacter urativorans)
- 30s ribosomal protein s30 (14 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl9 (18 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs16 (9 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs6 (15 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Psychrobacter urativorans)
- 16s rrna (514 kDa, RNA from Psychrobacter urativorans)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Psychrobacter urativorans)
- Elongation factor tu (43 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl32 (7 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us5 (18 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Psychrobacter urativorans)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8rdv
Q-score: 0.627
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV
Nature (2024) 626 pp. 1125-1132 [ Pubmed: 38355796 DOI: doi:10.1038/s41586-024-07041-8 ]
- Small ribosomal subunit protein us15 (10 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul22 (11 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us4 (24 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us2 (29 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul23 (12 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs18 (8 kDa, Protein from Psychrobacter urativorans)
- Heterogenous trna (23 kDa, RNA from Psychrobacter urativorans)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us3 (27 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl31b (10 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl25 (23 kDa, Protein from Psychrobacter urativorans)
- Methyl-accepting chemotaxis protein (41 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Psychrobacter urativorans)
- 5s rrna (36 kDa, RNA from Psychrobacter urativorans)
- Large ribosomal subunit protein ul4 (21 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Psychrobacter urativorans)
- Ribosomes isolated from ice-treated cultures of psychrobacter urativorans. (Complex from Psychrobacter urativorans)
- Large ribosomal subunit protein bl19 (14 kDa, Protein from Psychrobacter urativorans)
- Heterogenous mrna (1 kDa, RNA from Psychrobacter urativorans)
- Large ribosomal subunit protein ul5 (19 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul13 (15 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs16 (9 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl9 (18 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs6 (15 kDa, Protein from Psychrobacter urativorans)
- 23s rrna (933 kDa, RNA from Psychrobacter urativorans)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Psychrobacter urativorans)
- 16s rrna (514 kDa, RNA from Psychrobacter urativorans)
- Elongation factor tu (43 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl32 (7 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us5 (18 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Psychrobacter urativorans)
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8rdw
Q-score: 0.604
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV
Nature (2024) 626 pp. 1125-1132 [ DOI: doi:10.1038/s41586-024-07041-8 Pubmed: 38355796 ]
- Large ribosomal subunit protein ul5 (19 kDa, Protein from Psychrobacter urativorans)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl36 (4 kDa, Protein from Psychrobacter urativorans)
- Ribosomes isolated from ice-treated cultures of psychrobacter urativorans. (Complex from Psychrobacter urativorans)
- Large ribosomal subunit protein ul4 (21 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us2 (29 kDa, Protein from Psychrobacter urativorans)
- 5s rrna (36 kDa, RNA from Psychrobacter urativorans)
- Small ribosomal subunit protein us5 (18 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Psychrobacter urativorans)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us3 (27 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul13 (15 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl25 (23 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl12 (12 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us4 (24 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl19 (14 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Psychrobacter urativorans)
- 16s rrna (514 kDa, RNA from Psychrobacter urativorans)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs18 (8 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl9 (18 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl32 (7 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl31b (10 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Psychrobacter urativorans)
- Elongation factor tu (43 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul22 (11 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us17 (10 kDa, Protein from Psychrobacter urativorans)
- Methyl-accepting chemotaxis protein (41 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul23 (12 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul6 (19 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs6 (15 kDa, Protein from Psychrobacter urativorans)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein bs16 (9 kDa, Protein from Psychrobacter urativorans)
- Small ribosomal subunit protein us7 (17 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Psychrobacter urativorans)
- 23s rrna (933 kDa, RNA from Psychrobacter urativorans)
- Large ribosomal subunit protein ul2 (30 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Psychrobacter urativorans)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Psychrobacter urativorans)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8v9j
Q-score: 0.525
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV
Nature (2024) 626 pp. 1125-1132 [ Pubmed: 38355796 DOI: doi:10.1038/s41586-024-07041-8 ]
- 30s ribosomal protein s20 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s17 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l01 (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l18 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l10 (18 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l3 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l16 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l32 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l28 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s18 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Poly-u mrna (873 Da, RNA from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- 16s ribosomal rna (495 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l9 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 5s ribosomal rna (38 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l17 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s13 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s16 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s14 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s10 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Ribosome hibernation factor balon (msmeg_1130) (41 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l19 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l24 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l21 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s15 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s7 (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l36 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s3 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l25 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l29 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l35 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s19 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Pe/e deacylated phenylanaline-trna (24 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l11 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l30 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l37 (2 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s11 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s8 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s6 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s4 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l23 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s22 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l13 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l27 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l22 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s9 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 23s ribosomal rna (1 MDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l15 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l34 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l31 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l33 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cryo-em structure of the mycobacterium smegmatis 70s ribosome in complex with hibernation factor msmeg1130 (balon) (structure 4) (2 MDa, Complex from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l6 (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l20 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s12 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l4 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8v9k
Q-score: 0.461
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV
Nature (2024) 626 pp. 1125-1132 [ Pubmed: 38355796 DOI: doi:10.1038/s41586-024-07041-8 ]
- 30s ribosomal protein s20 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s17 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l10 (18 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l3 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl31 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l32 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl20 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Poly-u mrna (873 Da, RNA from Mycolicibacterium smegmatis MC2 155)
- 16s ribosomal rna (495 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l9 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 5s ribosomal rna (38 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l17 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s13 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s16 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s10 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul22 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l19 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l24 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul1 (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s7 (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Ribosome hibernation factor balon (rv2629) (40 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Large ribosomal subunit protein bl33a (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l36 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s3 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l25 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l29 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Small ribosomal subunit protein us14b (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Small ribosomal subunit protein us5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l35 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s19 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Pe/e deacylated phenylanaline-trna (24 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- Cryo-em structure of the mycobacterium smegmatis 70s ribosome in complex with hibernation factor rv2629 (balon) (structure 5) (2 MDa, Complex from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l11 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l30 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s11 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s6 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s4 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s22 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l27 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s9 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 23s ribosomal rna (1 MDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l15 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l34 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl28 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l6 (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l37 (2 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Small ribosomal subunit protein bs18b (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s12 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8v9l
Q-score: 0.527
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV
Nature (2024) 626 pp. 1125-1132 [ DOI: doi:10.1038/s41586-024-07041-8 Pubmed: 38355796 ]
- 30s ribosomal protein s22 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl33a (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s6 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl20 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l17 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s20 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l27 (2 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s16 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l25 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l29 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l32 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Zinc ion (65 Da, Ligand)
- Large ribosomal subunit protein ul22 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l11 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l36 (4 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l6 (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Pe/e deacylated phenylanaline-trna (24 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Elongation factor tu (43 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l19 (12 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s10 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s9 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 5s ribosomal rna (38 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s19 (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s13 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l27 (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 16s ribosomal rna (495 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s4 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l30 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l35 (7 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s7 (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l3 (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s12 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l9 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Poly-u mrna (1 kDa, RNA from Mycolicibacterium smegmatis MC2 155)
- Small ribosomal subunit protein us14b (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Ribosome hibernation factor balon (msmeg_1130) (41 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein ul18 (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl28 (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Large ribosomal subunit protein bl31 (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l2 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l34 (5 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Small ribosomal subunit protein us5 (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Small ribosomal subunit protein bs18b (9 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 23s ribosomal rna (1 MDa, RNA from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l24 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s11 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s3 (30 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l15 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 30s ribosomal protein s17 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- 50s ribosomal protein l10 (18 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cryo-em structure of the mycobacterium smegmatis 70s ribosome in complex with hibernation factor msmeg1130 (balon) and msmegef-tu(gdp) (composite structure 6) (2 MDa, Complex from Mycolicibacterium smegmatis MC2 155)
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV
Nature (2024) 626 pp. 1125-1132 [ DOI: doi:10.1038/s41586-024-07041-8 Pubmed: 38355796 ]
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV
Nature (2024) 626 pp. 1125-1132 [ DOI: doi:10.1038/s41586-024-07041-8 Pubmed: 38355796 ]
Candidatus Methanomethylophilus alvus tRNAPyl in A-site of ribosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8upt
Q-score: 0.441
Krahn N, Zhang J, Melnikov SV, Tharp JM, Villa A, Patel A, Howard RJ, Gabir H, Patel TR, Stetefeld J, Puglisi J, Soll D
Nucleic Acids Res (2024) 52 pp. 513-524 [ Pubmed: 38100361 DOI: doi:10.1093/nar/gkad1188 ]