Dibekacin-bound E.coli 70S ribosome in the PURE system
Resolution: 2.43 Å
EM Method: Single-particle
Fitted PDBs: 8ifb
Q-score: 0.662
Tomono J, Asano K, Chiashi T, Suzuki M, Igarashi M, Takahashi Y, Tanaka Y, Yokoyama T
J.Biochem. (2024) 175 pp. 587-598 [ Pubmed: 38227611 DOI: doi:10.1093/jb/mvae002 ]
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- Mrna (3 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- P-site trna-fmet (24 kDa, RNA from Escherichia coli)
- Dibekacin (451 Da, Ligand)
- Dbk-bound e.coli 70s ribosome in the pure system (2 MDa, Complex from Escherichia coli)
- Spermine (202 Da, Ligand)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- A-site trna-phe (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- Spermidine (145 Da, Ligand)
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
Arbekacin-bound E.coli 70S ribosome in the PURE system
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8ifc
Q-score: 0.62
Tomono J, Asano K, Chiashi T, Suzuki M, Igarashi M, Takahashi Y, Tanaka Y, Yokoyama T
J.Biochem. (2024) 175 pp. 587-598 [ Pubmed: 38227611 DOI: doi:10.1093/jb/mvae002 ]
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- Mrna (3 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- Spermine (202 Da, Ligand)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- A-site trna-phe (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- P-site trnaf-met (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- Spermidine (145 Da, Ligand)
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- Arbekacin (552 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- Abk-bound e.coli 70s ribosome (2 MDa, Complex from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
Cryo-EM structure of ATP13A2 in the E2P state
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8iem
Q-score: 0.262
Mu J, Xue C, Fu L, Yu Z, Nie M, Wu M, Chen X, Liu K, Bu R, Huang Y, Yang B, Han J, Jiang Q, Chan KC, Zhou R, Li H, Huang A, Wang Y, Liu Z
Nat Commun (2023) 14 pp. 1978-1978 [ DOI: doi:10.1038/s41467-023-37741-0 Pubmed: 37031211 ]
- Spermine (202 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Polyamine-transporting atpase 13a2 (123 kDa, Protein from Homo sapiens)
- Polyamine-transporting atpase 13a2 (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
Cryo-EM structure of ATP13A2 in the E2-Pi state
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8ien
Q-score: -0.047
Mu J, Xue C, Fu L, Yu Z, Nie M, Wu M, Chen X, Liu K, Bu R, Huang Y, Yang B, Han J, Jiang Q, Chan KC, Zhou R, Li H, Huang A, Wang Y, Liu Z
Nat Commun (2023) 14 pp. 1978-1978 [ DOI: doi:10.1038/s41467-023-37741-0 Pubmed: 37031211 ]
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Polyamine-transporting atpase 13a2 (128 kDa, Protein from Homo sapiens)
- Spermine (202 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cryo-em structure of atp13a2 in the e2-pi state (Complex from Homo sapiens)
Cryo-EM structure of ATP13A2 in the nominal E1P state
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 8ieo
Q-score: 0.312
Mu J, Xue C, Fu L, Yu Z, Nie M, Wu M, Chen X, Liu K, Bu R, Huang Y, Yang B, Han J, Jiang Q, Chan KC, Zhou R, Li H, Huang A, Wang Y, Liu Z
Nat Commun (2023) 14 pp. 1978-1978 [ DOI: doi:10.1038/s41467-023-37741-0 Pubmed: 37031211 ]
- Tetrafluoroaluminate ion (102 Da, Ligand)
- Polyamine-transporting atpase 13a2 (128 kDa, Protein from Homo sapiens)
- Spermine (202 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cryo-em structure of atp13a2 in the nominal e1p state (Complex from Homo sapiens)
Cryo-EM structure of ATP13A2 in the putative of E2 state
Resolution: 4.87 Å
EM Method: Single-particle
Fitted PDBs: 8ier
Q-score: 0.162
Mu J, Xue C, Fu L, Yu Z, Nie M, Wu M, Chen X, Liu K, Bu R, Huang Y, Yang B, Han J, Jiang Q, Chan KC, Zhou R, Li H, Huang A, Wang Y, Liu Z
Nat Commun (2023) 14 pp. 1978-1978 [ DOI: doi:10.1038/s41467-023-37741-0 Pubmed: 37031211 ]
- Spermine (202 Da, Ligand)
- Polyamine-transporting atpase 13a2 (128 kDa, Protein from Homo sapiens)
- Cryo-em structure of atp13a2 in the putative of e2 state (Complex from Homo sapiens)
Cryo-EM structure of the plant 80S ribosome
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8b2l
Q-score: 0.639
Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R
Nat Plants (2023) 9 pp. 987-1000 [ DOI: doi:10.1038/s41477-023-01407-y Pubmed: 37156858 ]
- 60s ribosomal protein l30-like (12 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s27 (9 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s2-3-like (30 kDa, Protein from Nicotiana tabacum)
- Nascent chain (2 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s21 (9 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s14-2 (16 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s5-like (23 kDa, Protein from Nicotiana tabacum)
- 30s ribosomal protein s15, chloroplastic (17 kDa, Protein from Nicotiana tabacum)
- 25s rrna (1 MDa, RNA from Nicotiana tabacum)
- 40s ribosomal protein s9-2-like (23 kDa, Protein from Nicotiana tabacum)
- Water (18 Da, Ligand)
- 40s ribosomal protein s10-1-like (23 kDa, Protein from Nicotiana tabacum)
- 5.8s rrna (52 kDa, RNA from Nicotiana tabacum)
- 60s ribosomal protein l18a (21 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l44 (12 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s19-3 (16 kDa, Protein from Nicotiana tabacum)
- Ul5 (60s ribosomal protein l11) (20 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l7a (29 kDa, Protein from Nicotiana tabacum)
- Ul3 (60s ribosomal protein l3) (44 kDa, Protein from Nicotiana tabacum)
- 50s ribosomal protein l22, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
- El36 (60s ribosomal protein l36) (12 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l23a (17 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s3-2-like (27 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s16 (16 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s15-like (17 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s15a-1 (14 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s8 (25 kDa, Protein from Nicotiana tabacum)
- Potassium ion (39 Da, Ligand)
- 40s ribosomal protein s20-2 (13 kDa, Protein from Nicotiana tabacum)
- Mrna (3 kDa, RNA from Nicotiana tabacum)
- 60s ribosomal protein l21-1-like (18 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l39-3 (6 kDa, Protein from Nicotiana tabacum)
- Ul4 (60s ribosomal protein l4) (44 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l24-like (18 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s18 (17 kDa, Protein from Nicotiana tabacum)
- El33 (60s ribosomal protein l35a) (12 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l35-like (14 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s12 (15 kDa, Protein from Nicotiana tabacum)
- Ubiquitin-40s ribosomal protein s27a-like (17 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l5-like (34 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s7 (22 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l37a (10 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l29 (7 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l18-2-like (20 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l32-1 (15 kDa, Protein from Nicotiana tabacum)
- El27 (60s ribosomal protein l27) (15 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l13 (23 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s3a (29 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s17-like (16 kDa, Protein from Nicotiana tabacum)
- Ul13 (60s ribosomal protein l13a) (23 kDa, Protein from Nicotiana tabacum)
- Guanine nucleotide-binding protein subunit beta-like protein (36 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s6 (28 kDa, Protein from Nicotiana tabacum)
- Ul16 (60s ribosomal protein l10) (25 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s24 (15 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s23 (15 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l23 (15 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- Ul24 (60s ribosomal protein l26) (16 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s25 (11 kDa, Protein from Nicotiana tabacum)
- El6 (60s ribosomal protein l6) (25 kDa, Protein from Nicotiana tabacum)
- El31 (60s ribosomal protein l31) (13 kDa, Protein from Nicotiana tabacum)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein sa (35 kDa, Protein from Nicotiana tabacum)
- El28 (60s ribosomal protein l28) (15 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l14-1 (15 kDa, Protein from Nicotiana tabacum)
- Ul2 (60s ribosomal protein l8) (28 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l7-4-like (28 kDa, Protein from Nicotiana tabacum)
- Trna (24 kDa, RNA from Nicotiana tabacum)
- Ul6 (60s ribosomal protein l9) (22 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s30 (6 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l41 (3 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s28 (7 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l34 (13 kDa, Protein from Nicotiana tabacum)
- Spermine (202 Da, Ligand)
- Ribosomal protein l19 (25 kDa, Protein from Nicotiana tabacum)
- 40s subunit of the cytosolic 80s ribosome from tobacco (Complex from Nicotiana tabacum)
- Zinc ion (65 Da, Ligand)
- 5s rrna (38 kDa, RNA from Nicotiana tabacum)
- 40s ribosomal protein s11-like (17 kDa, Protein from Nicotiana tabacum)
- Spermidine (145 Da, Ligand)
- 40s ribosomal protein s29 (6 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s26 (14 kDa, Protein from Nicotiana tabacum)
- Ul15 (60s ribosomal protein l27a) (16 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l38 (8 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s4 (29 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l22-2-like (14 kDa, Protein from Nicotiana tabacum)
- 18s rrna (583 kDa, RNA from Nicotiana tabacum)
- Ribosomal protein l37 (10 kDa, Protein from Nicotiana tabacum)
- Ribosomal protein l15 (24 kDa, Protein from Nicotiana tabacum)
Ternary complex of translating ribosome, NAC and METAP1
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8p2k
Q-score: 0.483
Gamerdinger M, Jia M, Schloemer R, Rabl L, Jaskolowski M, Khakzar KM, Ulusoy Z, Wallisch A, Jomaa A, Hunaeus G, Scaiola A, Diederichs K, Ban N, Deuerling E
Science (2023) 380 pp. 1238-1243 [ DOI: doi:10.1126/science.adg3297 Pubmed: 37347872 ]
- Ribosomal_l23en domain-containing protein (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
- Transcription factor btf3 (14 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
- 5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- 28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l30 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s5 (22 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l39-like (6 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s2 (31 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
- Water (18 Da, Ligand)
- 60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s9 (22 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul1 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l5 eukaryotic c-terminal domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s13 (17 kDa, Protein from Oryctolagus cuniculus)
- E-site trna (15 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s3a (30 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l37a (10 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l28 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3 (31 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
- 5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul30 (29 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s18 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l32 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- Any 5'-monophosphate nucleotide (214 Da, Ligand)
- 60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l31 (14 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s14 (16 kDa, Protein from Oryctolagus cuniculus)
- Methionine aminopeptidase 1 (43 kDa, Protein from Homo sapiens)
- Ternary complex of translating ribosome, nac and metap1 (Complex from Oryctolagus cuniculus)
- Ribosome translating a cytosolic peptide (Complex from Homo sapiens)
- Nascent polypeptide-associated complex subunit alpha (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s29 (6 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s7 (47 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (28 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Oryctolagus cuniculus)
- Unknown atom or ion (Ligand)
- Acetylamino-acetic acid (117 Da, Ligand)
- Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- Us9 (19 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s19 (16 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
- P-site val-trna (24 kDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
- El18 (21 kDa, Protein from Oryctolagus cuniculus)
- Spermine (202 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l7a (30 kDa, Protein from Oryctolagus cuniculus)
- Es26 (13 kDa, Protein from Oryctolagus cuniculus)
- Spermidine (145 Da, Ligand)
- Glucose-6-phosphate isomerase (7 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
- Complex of nac and metap1 at the tennel exit of translating ribosome (Complex)
- 40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- S10_plectin domain-containing protein (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l22 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s27a (18 kDa, Protein from Oryctolagus cuniculus)
Cryo-EM structure of the plant 40S subunit
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 8auv
Q-score: 0.622
Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R
Nat Plants (2023) 9 pp. 987-1000 [ DOI: doi:10.1038/s41477-023-01407-y Pubmed: 37156858 ]
- Es4 (40s ribosomal protein s4) (29 kDa, Protein from Nicotiana tabacum)
- Es10 (40s ribosomal protein s10) (23 kDa, Protein from Nicotiana tabacum)
- Es6 (40s ribosomal protein s6) (28 kDa, Protein from Nicotiana tabacum)
- Us11 (40s ribosomal protein s14) (16 kDa, Protein from Nicotiana tabacum)
- Us13 (40s ribosomal protein s18) (17 kDa, Protein from Nicotiana tabacum)
- Es31 (ubiquitin-40s ribosomal protein s27a) (17 kDa, Protein from Nicotiana tabacum)
- Es8 (40s ribosomal protein s8) (25 kDa, Protein from Nicotiana tabacum)
- Us15 (40s ribosomal protein s13) (17 kDa, Protein from Nicotiana tabacum)
- Es24 (40s ribosomal protein s24) (15 kDa, Protein from Nicotiana tabacum)
- Us4 (40s ribosomal protein s9) (23 kDa, Protein from Nicotiana tabacum)
- Us14 (40s ribosomal protein s29) (6 kDa, Protein from Nicotiana tabacum)
- Es17 (40s ribosomal protein s17) (16 kDa, Protein from Nicotiana tabacum)
- Us2 (40s ribosomal protein sa) (35 kDa, Protein from Nicotiana tabacum)
- Us19 (40s ribosomal protein s15) (17 kDa, Protein from Nicotiana tabacum)
- Us9 (40s ribosomal protein s16) (16 kDa, Protein from Nicotiana tabacum)
- Es12 (40s ribosomal protein s12) (15 kDa, Protein from Nicotiana tabacum)
- Us10 (40s ribosomal protein s20) (13 kDa, Protein from Nicotiana tabacum)
- Es21 (40s ribosomal protein s21) (9 kDa, Protein from Nicotiana tabacum)
- Spermine (202 Da, Ligand)
- Es26 (40s ribosomal protein s26) (14 kDa, Protein from Nicotiana tabacum)
- 40s subunit of the cytosolic 80s ribosome from tobacco (Complex from Nicotiana tabacum)
- Us7 (40s ribosomal protein s5) (23 kDa, Protein from Nicotiana tabacum)
- Potassium ion (39 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Mrna (3 kDa, RNA from Nicotiana tabacum)
- Es27 (40s ribosomal protein s27) (9 kDa, Protein from Nicotiana tabacum)
- Spermidine (145 Da, Ligand)
- Es30 (40s ribosomal protein s30) (6 kDa, Protein from Nicotiana tabacum)
- Es19 (40s ribosomal protein s19) (16 kDa, Protein from Nicotiana tabacum)
- Us3 (40s ribosomal protein s3) (27 kDa, Protein from Nicotiana tabacum)
- Es7 (40s ribosomal protein s7) (22 kDa, Protein from Nicotiana tabacum)
- Rack1 (guanine nucleotide-binding protein subunit beta-like protein) (36 kDa, Protein from Nicotiana tabacum)
- Water (18 Da, Ligand)
- Us17 (40s ribosomal protein s11) (17 kDa, Protein from Nicotiana tabacum)
- Us12 (40s ribosomal protein s23) (15 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- Es1 (40s ribosomal protein s3a) (29 kDa, Protein from Nicotiana tabacum)
- Us8 (40s ribosomal protein s15a) (14 kDa, Protein from Nicotiana tabacum)
- Es25 (40s ribosomal protein s25) (11 kDa, Protein from Nicotiana tabacum)
- 18s rrna (583 kDa, RNA from Nicotiana tabacum)
- Es28 (40s ribosomal protein s28) (7 kDa, Protein from Nicotiana tabacum)
- Us5 (40s ribosomal protein s2) (30 kDa, Protein from Nicotiana tabacum)
Cryo-EM structure of the plant 60S subunit
Resolution: 2.14 Å
EM Method: Single-particle
Fitted PDBs: 8azw
Q-score: 0.675
Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R
Nat Plants (2023) 9 pp. 987-1000 [ DOI: doi:10.1038/s41477-023-01407-y Pubmed: 37156858 ]
- El20 (60s ribosomal protein l18a) (21 kDa, Protein from common tobacco)
- Nascent chain (2 kDa, Protein from common tobacco)
- El19 (60s ribosomal protein l19) (25 kDa, Protein from common tobacco)
- Ul13 (60s ribosomal protein l13a) (23 kDa, Protein from common tobacco)
- El22 (60s ribosomal protein l22) (14 kDa, Protein from common tobacco)
- Ul2 (60s ribosomal protein l8) (28 kDa, Protein from common tobacco)
- Ul5 (60s ribosomal protein l11) (20 kDa, Protein from common tobacco)
- Ul16 (60s ribosomal protein l10) (25 kDa, Protein from common tobacco)
- El39 (60s ribosomal protein l39) (6 kDa, Protein from common tobacco)
- Ul30 (60s ribosomal protein l7) (28 kDa, Protein from common tobacco)
- El6 (60s ribosomal protein l6) (25 kDa, Protein from common tobacco)
- Ul4 (60s ribosomal protein l4) (44 kDa, Protein from common tobacco)
- Spermine (202 Da, Ligand)
- 40s subunit of the cytosolic 80s ribosome from tobacco (Complex from Nicotiana tabacum)
- El15 (60s ribosomal protein l15) (24 kDa, Protein from common tobacco)
- El36 (60s ribosomal protein l36) (12 kDa, Protein from common tobacco)
- Potassium ion (39 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- El29 (60s ribosomal protein l29) (7 kDa, Protein from common tobacco)
- El30 (60s ribosomal protein l30) (12 kDa, Protein from common tobacco)
- Ul15 (60s ribosomal protein l27a) (16 kDa, Protein from common tobacco)
- Ul29 (60s ribosomal protein l35) (14 kDa, Protein from common tobacco)
- Spermidine (145 Da, Ligand)
- El40 (60s ribosomal protein l40) (14 kDa, Protein from common tobacco)
- El42 (60s ribosomal protein l42) (12 kDa, Protein from common tobacco)
- El33 (60s ribosomal protein l35a) (12 kDa, Protein from common tobacco)
- El41 (60s ribosomal protein l41) (3 kDa, Protein from common tobacco)
- Ul6 (60s ribosomal protein l9) (22 kDa, Protein from common tobacco)
- Water (18 Da, Ligand)
- El37 (60s ribosomal protein l37) (10 kDa, Protein from common tobacco)
- Ul18 (60s ribosomal protein l5) (34 kDa, Protein from common tobacco)
- 25s rrna (1 MDa, RNA from common tobacco)
- Magnesium ion (24 Da, Ligand)
- Ul22 (60s ribosomal protein l17) (20 kDa, Protein from common tobacco)
- El28 (60s ribosomal protein l28) (15 kDa, Protein from common tobacco)
- El14 (60s ribosomal protein l14) (15 kDa, Protein from common tobacco)
- El32 (60s ribosomal protein l32) (15 kDa, Protein from common tobacco)
- Ul24 (60s ribosomal protein l26) (16 kDa, Protein from common tobacco)
- El13 (60s ribosomal protein l13) (23 kDa, Protein from common tobacco)
- El21 (60s ribosomal protein l21) (18 kDa, Protein from common tobacco)
- Ul3 (60s ribosomal protein l3) (44 kDa, Protein from common tobacco)
- El34 (60s ribosomal protein l34) (13 kDa, Protein from common tobacco)
- El18 (60s ribosomal protein l18) (20 kDa, Protein from common tobacco)
- El43 (60s ribosomal protein l37a) (10 kDa, Protein from common tobacco)
- Ul14 (60s ribosomal protein l23) (15 kDa, Protein from common tobacco)
- Ul23 (60s ribosomal protein l23a) (17 kDa, Protein from common tobacco)
- El27 (60s ribosomal protein l27) (15 kDa, Protein from common tobacco)
- 5s rrna (38 kDa, RNA from common tobacco)
- 5.8s rrna (52 kDa, RNA from common tobacco)
- El8 (60s ribosomal protein l7a) (29 kDa, Protein from common tobacco)
- El38 (60s ribosomal protein l38) (8 kDa, Protein from common tobacco)
- El31 (60s ribosomal protein l31) (13 kDa, Protein from common tobacco)
- El24 (60s ribosomal protein l24) (18 kDa, Protein from common tobacco)