Yeast 80S, ES7s delta, eIF5A, Stm1 containing
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8bn3
Q-score: 0.597
Rauscher R, Eggers C, Dimitrova-Paternoga L, Shankar V, Rosina A, Cristodero M, Paternoga H, Wilson DN, Leidel SA, Polacek N
Nucleic Acids Res (2024) 52 pp. 4021-4036 [ DOI: doi:10.1093/nar/gkae067 Pubmed: 38324474 ]
- Small ribosomal subunit protein us2a (27 kDa, Protein from Saccharomyces cerevisiae)
- Rps15 isoform 1 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l8-a (25 kDa, Protein from Saccharomyces cerevisiae)
- Rpl4a isoform 1 (39 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (25 kDa, Protein from Saccharomyces cerevisiae)
- Rps28a isoform 1 (7 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae)
- Rps2 isoform 1 (23 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Large ribosomal subunit protein el37a (9 kDa, Protein from Saccharomyces cerevisiae)
- Ribosomal protein l15 (24 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us17a (17 kDa, Protein from Saccharomyces cerevisiae)
- Rpl5 isoform 1 (33 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)
- Small ribosomal subunit protein es21a (9 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l22-a (11 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein us4a (21 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es4a (29 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s13 (16 kDa, Protein from Saccharomyces cerevisiae)
- Es17 (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l43-a (9 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es1 (24 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- Rps26b isoform 1 (11 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el41b (3 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l25 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dormant yeast 80s ribosome (3 MDa, Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae)
- Stm1 isoform 1 (12 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein rack1 (34 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae)
- Rpl32 isoform 1 (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s8 (21 kDa, Protein from Saccharomyces cerevisiae)
- 5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae)
- Rps22a isoform 1 (14 kDa, Protein from Saccharomyces cerevisiae)
- Eukaryotic translation initiation factor 5a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s18-a (16 kDa, Protein from Saccharomyces cerevisiae)
- Rpl10 isoform 1 (24 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l40-a (6 kDa, Protein from Saccharomyces cerevisiae)
- Rpl11b isoform 1 (19 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es10a (11 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l1-a (24 kDa, Protein from Saccharomyces cerevisiae)
- 25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein el34a (12 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae)
- 4-{(2r)-2-[(1s,3s,5s)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione (281 Da, Ligand)
- 18s ribosomal rna (559 kDa, RNA from Saccharomyces cerevisiae)
- Rps31 isoform 1 (8 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l13-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s14-b (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l6-a (17 kDa, Protein from Saccharomyces cerevisiae)
- 5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
- Rpl24a isoform 1 (11 kDa, Protein from Saccharomyces cerevisiae)
- Rpl9a isoform 1 (21 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l41-a (2 kDa, Protein from Saccharomyces cerevisiae)
- Rps5p (22 kDa, Protein from Saccharomyces cerevisiae)
- Rps29a isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l14-a (14 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l29 (6 kDa, Protein from Saccharomyces cerevisiae)
- Small ribosomal subunit protein es6a (25 kDa, Protein from Saccharomyces cerevisiae)
- Rpl38 isoform 1 (8 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Rps20 isoform 1 (12 kDa, Protein from Saccharomyces cerevisiae)
- Spermidine (145 Da, Ligand)
- 40s ribosomal protein s25 (8 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s3 (24 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l42-a (12 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s30-a (6 kDa, Protein from Saccharomyces cerevisiae)
- Large ribosomal subunit protein ul24a (14 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s23-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 60s ribosomal protein l30 (10 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7zta
Q-score: 0.565
Leroy EC, Perry TN, Renault TT, Innis CA
Nat Chem Biol (2023) 19 pp. 1091-1096 [ DOI: doi:10.1038/s41589-023-01343-0 Pubmed: 37322159 ]
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal subunit (Complex from Escherichia coli K-12)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli K-12)
- Trna-gln (e site) (Complex from Escherichia coli K-12)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli K-12)
- Maaapqk nascent peptide (716 Da, Protein from Escherichia coli K-12)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli K-12)
- Cysteine (121 Da, Ligand)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli K-12)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli K-12)
- Structure of an escherichia coli 70s ribosome stalled by tetracenomycin x during translation of an maaapqk(c) peptide (Complex from Escherichia coli K-12)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli K-12)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli K-12)
- Mrna (Complex from Escherichia coli K-12)
- Mrna (4 kDa, RNA from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Tetracenomycin x (486 Da, Ligand)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal subunit (Complex from Escherichia coli K-12)
- Trna-cys (a site) (Complex from Escherichia coli K-12)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli K-12)
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli K-12)
- 50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s21 (6 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli K-12)
- Water (18 Da, Ligand)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli K-12)
- Trna-cys (23 kDa, RNA from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli K-12)
- Trna-lys (24 kDa, RNA from Escherichia coli K-12)
- Trna-gln (24 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli K-12)
- Maaapqk-trna-lys (p site) (Complex)
- Glutamine (146 Da, Ligand)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli K-12)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli K-12)
- 30s ribosomal protein s6, fully modified isoform (12 kDa, Protein from Escherichia coli K-12)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli K-12)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7zrd
Q-score: 0.504
Silberberg JM, Stock C, Hielkema L, Corey RA, Rheinberger J, Wunnicke D, Dubach VRA, Stansfeld PJ, Hanelt I, Paulino C
eLife (2022) 11 [ Pubmed: 36255052 DOI: doi:10.7554/eLife.80988 ]
- Kdpfabc (157 kDa, Complex from Escherichia coli)
- Potassium-transporting atpase kdpc subunit (20 kDa, Protein from Escherichia coli)
- Potassium-transporting atpase atp-binding subunit (72 kDa, Protein from Escherichia coli)
- Cardiolipin (1 kDa, Ligand)
- Potassium ion (39 Da, Ligand)
- Potassium-transporting atpase kdpf subunit (3 kDa, Protein from Escherichia coli)
- Vanadate ion (114 Da, Ligand)
- Potassium-transporting atpase potassium-binding subunit (59 kDa, Protein from Escherichia coli)
Cryo-EM map of the WT KdpFABC complex in the E1-P tight conformation, under turnover conditions
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7zre
Q-score: 0.487
Silberberg JM, Stock C, Hielkema L, Corey RA, Rheinberger J, Wunnicke D, Dubach VRA, Stansfeld PJ, Hanelt I, Paulino C
eLife (2022) 11 [ Pubmed: 36255052 DOI: doi:10.7554/eLife.80988 ]
- Potassium-transporting atpase kdpf subunit (2 kDa, Protein from Escherichia coli)
- Potassium-transporting atpase atp-binding subunit (72 kDa, Protein from Escherichia coli)
- Kdpfabc (157 kDa, Complex from Escherichia coli)
- Potassium-transporting atpase kdpc subunit (20 kDa, Protein from Escherichia coli)
- Cardiolipin (1 kDa, Ligand)
- Potassium ion (39 Da, Ligand)
- Potassium-transporting atpase potassium-binding subunit (59 kDa, Protein from Escherichia coli)
Cryo-EM map of the WT KdpFABC complex in the E1_ATPearly conformation, under turnover conditions
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7zrg
Q-score: 0.465
Silberberg JM, Stock C, Hielkema L, Corey RA, Rheinberger J, Wunnicke D, Dubach VRA, Stansfeld PJ, Hanelt I, Paulino C
eLife (2022) 11 [ Pubmed: 36255052 DOI: doi:10.7554/eLife.80988 ]
- Potassium-transporting atpase kdpf subunit (2 kDa, Protein from Escherichia coli)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Kdpfabc (157 kDa, Complex from Escherichia coli)
- Potassium-transporting atpase kdpc subunit (20 kDa, Protein from Escherichia coli)
- Potassium-transporting atpase atp-binding subunit (72 kDa, Protein from Escherichia coli)
- Cardiolipin (1 kDa, Ligand)
- Potassium ion (39 Da, Ligand)
- Potassium-transporting atpase potassium-binding subunit (59 kDa, Protein from Escherichia coli)
Cryo-EM structure of the KdpFABC complex in a nucleotide-free E1 conformation loaded with K+
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7zrh
Q-score: 0.485
Silberberg JM, Stock C, Hielkema L, Corey RA, Rheinberger J, Wunnicke D, Dubach VRA, Stansfeld PJ, Hanelt I, Paulino C
eLife (2022) 11 [ Pubmed: 36255052 DOI: doi:10.7554/eLife.80988 ]
- Potassium-transporting atpase atp-binding subunit (72 kDa, Protein from Escherichia coli)
- Potassium-transporting atpase kdpf subunit (2 kDa, Protein from Escherichia coli)
- Kdpfabc (157 kDa, Complex from Escherichia coli)
- Potassium-transporting atpase kdpc subunit (20 kDa, Protein from Escherichia coli)
- Cardiolipin (1 kDa, Ligand)
- Potassium ion (39 Da, Ligand)
- Potassium-transporting atpase potassium-binding subunit (59 kDa, Protein from Escherichia coli)
Cryo-EM structure of the KdpFABC complex in a nucleotide-free E1 conformation loaded with K+
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7zri
Q-score: 0.457
Silberberg JM, Stock C, Hielkema L, Corey RA, Rheinberger J, Wunnicke D, Dubach VRA, Stansfeld PJ, Hanelt I, Paulino C
eLife (2022) 11 [ Pubmed: 36255052 DOI: doi:10.7554/eLife.80988 ]
- Potassium-transporting atpase atp-binding subunit (72 kDa, Protein from Escherichia coli)
- Potassium-transporting atpase kdpf subunit (2 kDa, Protein from Escherichia coli)
- Kdpfabc (157 kDa, Complex from Escherichia coli)
- Potassium-transporting atpase kdpc subunit (20 kDa, Protein from Escherichia coli)
- Cardiolipin (1 kDa, Ligand)
- Potassium ion (39 Da, Ligand)
- Potassium-transporting atpase potassium-binding subunit (59 kDa, Protein from Escherichia coli)
Cryo-EM structure of the KdpFABC complex in a nucleotide-free E1 conformation loaded with K+
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7zrj
Q-score: 0.429
Silberberg JM, Stock C, Hielkema L, Corey RA, Rheinberger J, Wunnicke D, Dubach VRA, Stansfeld PJ, Hanelt I, Paulino C
eLife (2022) 11 [ Pubmed: 36255052 DOI: doi:10.7554/eLife.80988 ]
- Potassium-transporting atpase atp-binding subunit (72 kDa, Protein from Escherichia coli)
- Potassium-transporting atpase kdpf subunit (2 kDa, Protein from Escherichia coli)
- Kdpfabc (157 kDa, Complex from Escherichia coli)
- Potassium-transporting atpase kdpc subunit (20 kDa, Protein from Escherichia coli)
- Cardiolipin (1 kDa, Ligand)
- Potassium ion (39 Da, Ligand)
- Potassium-transporting atpase potassium-binding subunit (59 kDa, Protein from Escherichia coli)
Cryo-EM map of the WT KdpFABC complex in the E1-P_ADP conformation, under turnover conditions
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7zrk
Q-score: 0.529
Silberberg JM, Stock C, Hielkema L, Corey RA, Rheinberger J, Wunnicke D, Dubach VRA, Stansfeld PJ, Hanelt I, Paulino C
eLife (2022) 11 [ Pubmed: 36255052 DOI: doi:10.7554/eLife.80988 ]
- Potassium-transporting atpase kdpf subunit (2 kDa, Protein from Escherichia coli)
- Potassium-transporting atpase atp-binding subunit (72 kDa, Protein from Escherichia coli)
- Kdpfabc (157 kDa, Complex from Escherichia coli)
- Potassium-transporting atpase kdpc subunit (20 kDa, Protein from Escherichia coli)
- Cardiolipin (1 kDa, Ligand)
- Potassium ion (39 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Potassium-transporting atpase potassium-binding subunit (59 kDa, Protein from Escherichia coli)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7zrl
Q-score: 0.42
Silberberg JM, Stock C, Hielkema L, Corey RA, Rheinberger J, Wunnicke D, Dubach VRA, Stansfeld PJ, Hanelt I, Paulino C
eLife (2022) 11 [ Pubmed: 36255052 DOI: doi:10.7554/eLife.80988 ]
- Potassium-transporting atpase kdpc subunit (20 kDa, Protein from Escherichia coli K-12)
- Kdpfabc (157 kDa, Complex from Escherichia coli K-12)
- Potassium-transporting atpase kdpf subunit (2 kDa, Protein from Escherichia coli K-12)
- Potassium ion (39 Da, Ligand)
- Potassium-transporting atpase potassium-binding subunit (59 kDa, Protein from Escherichia coli K-12)
- Potassium-transporting atpase atp-binding subunit (72 kDa, Protein from Escherichia coli K-12)