Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 6xiq
Q-score: 0.33
Zhou Y, Kastritis PL, Dougherty SE, Bouvette J, Hsu AL, Burbaum L, Mosalaganti S, Pfeffer S, Hagen WJH, Forster F, Borgnia MJ, Vogel C, Beck M, Bartesaghi A, Silva GM
PNAS (2020) 117 pp. 22157-22166 [ DOI: doi:10.1073/pnas.2005301117 Pubmed: 32855298 ]
- Rpp0 isoform 1 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- Rpl4a isoform 1 (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Rps1a isoform 1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Rpl38 isoform 1 (8 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 35s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
- Rpl9a isoform 1 (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s17-b (15 kDa, Protein from Saccharomyces cerevisiae)
- Rps29a isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- Rpl29 isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 18s ribosomal rna (579 kDa, RNA from Saccharomyces cerevisiae)
- 5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
- Rps2 isoform 1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Rps20 isoform 1 (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Rpl24a isoform 1 (17 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Rps26b isoform 1 (13 kDa, Protein from Saccharomyces cerevisiae)
- Rps8a isoform 1 (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
- 40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
- K63 ubiquitinated ribosome (3 MDa, Complex from Saccharomyces cerevisiae)
- Rpl11b isoform 1 (19 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Rps25a isoform 1 (12 kDa, Protein from Saccharomyces cerevisiae)
- Rps5p (25 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
- Transfer rna (24 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- Rpl8a isoform 1 (28 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Rpl3 isoform 1 (43 kDa, Protein from Saccharomyces cerevisiae)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
- Mrna (2 kDa, RNA from Saccharomyces cerevisiae)
- Rpl10 isoform 1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Rps28a isoform 1 (7 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- Rpl12a isoform 1 (17 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
- Rpl41a isoform 1 (3 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Rps22a isoform 1 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae)
- Rpl32 isoform 1 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s14-b (14 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- Rpl5 isoform 1 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
- Rpl1a isoform 1 (24 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6xir
Q-score: 0.405
Zhou Y, Kastritis PL, Dougherty SE, Bouvette J, Hsu AL, Burbaum L, Mosalaganti S, Pfeffer S, Hagen WJH, Forster F, Borgnia MJ, Vogel C, Beck M, Bartesaghi A, Silva GM
PNAS (2020) 117 pp. 22157-22166 [ DOI: doi:10.1073/pnas.2005301117 Pubmed: 32855298 ]
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae)
- 18s ribosomal rna (579 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- Rpl4a isoform 1 (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae)
- Rps25a isoform 1 (12 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Rpl41a isoform 1 (3 kDa, Protein from Saccharomyces cerevisiae)
- Rpl5 isoform 1 (33 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae)
- Rpl38 isoform 1 (8 kDa, Protein from Saccharomyces cerevisiae)
- Rpl24a isoform 1 (17 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Rps28a isoform 1 (7 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Rps22a isoform 1 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae)
- Rpl29 isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae)
- Rps26b isoform 1 (13 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s17-b (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s14-b (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae)
- Rpl8a isoform 1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Rps3 isoform 1 (26 kDa, Protein from Saccharomyces cerevisiae)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
- Rpl11b isoform 1 (19 kDa, Protein from Saccharomyces cerevisiae)
- Rpl9a isoform 1 (21 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
- K63 ubiquitinated ribosome (Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- Rps8a isoform 1 (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae)
- Rps20 isoform 1 (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae)
- Rps2 isoform 1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Rps29a isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s6-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s4-a (29 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- Rpl32 isoform 1 (14 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae)
- Rpl10 isoform 1 (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
- Rps1a isoform 1 (28 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae)
- Rps5p (25 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- Rpl3 isoform 1 (43 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae)
- Transfer rna (24 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 35s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
K.lactis 80S ribosome with p/PE tRNA and eIF5B
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6uz7
Q-score: 0.39
PNAS (2020) 117 pp. 1429-1437 [ Pubmed: 31900355 DOI: doi:10.1073/pnas.1916436117 ]
- 40s ribosomal protein s21 (9 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l24 (17 kDa, Protein from Kluyveromyces lactis)
- Klla0d05181p (13 kDa, Protein from Kluyveromyces lactis)
- Klla0b01474p (15 kDa, Protein from Kluyveromyces lactis)
- Klla0e06997p (14 kDa, Protein from Kluyveromyces lactis)
- Klla0b07139p (39 kDa, Protein from Kluyveromyces lactis)
- Klla0d03410p (27 kDa, Protein from Kluyveromyces lactis)
- Rps23 (16 kDa, Protein from Kluyveromyces lactis)
- Klla0f04499p (21 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s12 (14 kDa, Protein from Kluyveromyces lactis)
- Klla0b01562p (17 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s7 (21 kDa, Protein from Kluyveromyces lactis)
- Klla0f08261p (19 kDa, Protein from Kluyveromyces lactis)
- Klla0d10659p (25 kDa, Protein from Kluyveromyces lactis)
- Klla0c08371p (14 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l25 (15 kDa, Protein from Kluyveromyces lactis)
- Klla0e12277p (35 kDa, Protein from Kluyveromyces lactis)
- Klla0b08173p (12 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s27 (8 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l3 (43 kDa, Protein from Kluyveromyces lactis)
- Ribosomal protein l37 (9 kDa, Protein from Kluyveromyces lactis)
- Klla0b13409p (15 kDa, Protein from Kluyveromyces lactis)
- Ubiquitin fusion protein (14 kDa, Protein from Kluyveromyces lactis)
- 18s ribosomal rna (579 kDa, RNA from Kluyveromyces lactis)
- Ribosomal protein (24 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l44 (12 kDa, Protein from Kluyveromyces lactis)
- 60s acidic ribosomal protein p0 (33 kDa, Protein from Kluyveromyces lactis)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- 40s ribosomal protein s30 (7 kDa, Protein from Kluyveromyces lactis)
- Klla0f23265p (108 kDa, Protein from Kluyveromyces lactis)
- Klla0f25542p (13 kDa, Protein from Kluyveromyces lactis)
- 5.8s ribosomal rna (910 kDa, RNA from Kluyveromyces lactis)
- Kluyveromyces lactis 80s ribosome in complex with eif5b (Complex from Kluyveromyces lactis)
- Klla0d06941p (33 kDa, Protein from Kluyveromyces lactis)
- Ribosomal protein l15 (24 kDa, Protein from Kluyveromyces lactis)
- Klla0b04686p (20 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s24 (15 kDa, Protein from Kluyveromyces lactis)
- Ubiquitin-40s ribosomal protein s27a (17 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s16 (15 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s4 (29 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s1 (28 kDa, Protein from Kluyveromyces lactis)
- 25s ribosomal rna (1 MDa, RNA from Kluyveromyces lactis)
- Klla0f05247p (14 kDa, Protein from Kluyveromyces lactis)
- Klla0f07843p (15 kDa, Protein from Kluyveromyces lactis)
- Klla0d08305p (26 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l13 (22 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s14 (14 kDa, Protein from Kluyveromyces lactis)
- Klla0f18040p (16 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s28 (7 kDa, Protein from Kluyveromyces lactis)
- Gdpcp (12 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l39 (6 kDa, Protein from Kluyveromyces lactis)
- Klla0e12453p (21 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s0 (28 kDa, Protein from Kluyveromyces lactis)
- Klla0b05742p (14 kDa, Protein from Kluyveromyces lactis)
- Klla0e23673p (21 kDa, Protein from Kluyveromyces lactis)
- Klla0a07194p (15 kDa, Protein from Kluyveromyces lactis)
- Klla0e00573p (28 kDa, Protein from Kluyveromyces lactis)
- Rna (76-mer) (24 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (7 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l30 (11 kDa, Protein from Kluyveromyces lactis)
- Klla0c18216p (8 kDa, Protein from Kluyveromyces lactis)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s22 (14 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l36 (11 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s26 (13 kDa, Protein from Kluyveromyces lactis)
- Klla0a06336p (20 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l20 (20 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s29 (6 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s6 (26 kDa, Protein from Kluyveromyces lactis)
- Klla0d05643p (25 kDa, Protein from Kluyveromyces lactis)
- Klla0a07227p (20 kDa, Protein from Kluyveromyces lactis)
- Klla0d07405p (12 kDa, Protein from Kluyveromyces lactis)
- Klla0b02937p (13 kDa, Protein from Kluyveromyces lactis)
- Klla0a10483p (17 kDa, Protein from Kluyveromyces lactis)
- Klla0d16027p (27 kDa, Protein from Kluyveromyces lactis)
- Rpl28 (16 kDa, Protein from Kluyveromyces lactis)
- Klla0e23651p (18 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s8 (22 kDa, Protein from Kluyveromyces lactis)
- 40s ribosomal protein s25 (12 kDa, Protein from Kluyveromyces lactis)
- Klla0e03455p (15 kDa, Protein from Kluyveromyces lactis)
- Klla0f04675p (22 kDa, Protein from Kluyveromyces lactis)
- Rna (121-mer) (38 kDa, RNA from Kluyveromyces lactis)
- Klla0f09812p (27 kDa, Protein from Kluyveromyces lactis)
- 60s ribosomal protein l41 (3 kDa, Protein from Kluyveromyces lactis)
- Klla0e05941p (9 kDa, Protein from Kluyveromyces lactis)
- Klla0e06843p (14 kDa, Protein from Kluyveromyces lactis)