Ternary complex of ribosome nascent chain with SRP and NAC
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 7qwq
Q-score: 0.426
Jomaa A, Gamerdinger M, Hsieh HH, Wallisch A, Chandrasekaran V, Ulusoy Z, Scaiola A, Hegde RS, Shan SO, Ban N, Deuerling E
Science (2022) 375 pp. 839-844 [ DOI: doi:10.1126/science.abl6459 Pubmed: 35201867 ]
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- L8 (26 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (11 kDa, Protein from Oryctolagus cuniculus)
- Nascent polypeptide-associated complex subunit alpha (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- Ul30 (26 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l39 (6 kDa, Protein from Oryctolagus cuniculus)
- Srp rna 7sl (Complex from Homo sapiens)
- Ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l30 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- Nascent chain preprolactin (Complex from Homo sapiens)
- Ribosomal protein l32 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13a (56 kDa, Protein from Oryctolagus cuniculus)
- 28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l17 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (24 kDa, Protein from Oryctolagus cuniculus)
- 5s ribosomal rna (38 kDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l7a (36 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
- Nascent chain preprolactin (9 kDa, Protein from Homo sapiens)
- Signal recognition particle subunit srp68 (70 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin a-52 residue ribosomal protein fusion product 1 (14 kDa, Protein from Oryctolagus cuniculus)
- Isoform 2 of transcription factor btf3 (Complex from Homo sapiens)
- Ribosome (Complex from Oryctolagus cuniculus)
- 60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
- Signal recognition particle 54 kda protein (55 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l28 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- El42 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l23en domain-containing protein (17 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- Signal recognition particle proteins (Complex from Homo sapiens)
- El43 (10 kDa, Protein from Oryctolagus cuniculus)
- Srp rna 7sl (54 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- Ternary ribosome-nascent chain srp nac complex (Complex)
- Isoform 2 of transcription factor btf3 (17 kDa, Protein from Homo sapiens)
- El18 (21 kDa, Protein from Oryctolagus cuniculus)
- Ul3 (46 kDa, Protein from Homo sapiens)
- Ribosomal protein l31 (14 kDa, Protein from Oryctolagus cuniculus)
- Signal recognition particle 19 kda protein (16 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- 5.8s ribosomal rna (50 kDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein l22 (11 kDa, Protein from Oryctolagus cuniculus)
55S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E)
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7nsi
Q-score: 0.228
Kummer E, Schubert KN, Schoenhut T, Scaiola A, Ban N
Mol Cell (2021) 81 pp. 2566-2582.e6 [ Pubmed: 33878294 DOI: doi:10.1016/j.molcel.2021.03.042 ]
- Mrna (1 kDa, RNA from Sus scrofa)
- Death associated protein 3 (46 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l15, mitochondrial (33 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l43, mitochondrial isoform x2 (17 kDa, Protein from Sus scrofa)
- 16s rrna (504 kDa, RNA from Sus scrofa)
- Mitochondrial ribosomal protein s27 (51 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l10, mitochondrial isoform a (29 kDa, Protein from Sus scrofa)
- Ribosome-recycling factor, mitochondrial (28 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s31, mitochondrial (44 kDa, Protein from Sus scrofa)
- Water (18 Da, Ligand)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Sus scrofa)
- Ml53 (12 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l33, mitochondrial (7 kDa, Protein from Sus scrofa)
- 39s ribosomal protein s30, mitochondrial (49 kDa, Protein from Sus scrofa)
- Pentatricopeptide repeat domain 3,pentatricopeptide repeat domain 3,ms39,pentatricopeptide repeat domain 3,pentatricopeptide repeat domain 3 (76 kDa, Protein from Sus scrofa)
- Trna (p/e) (21 kDa, RNA from Sus scrofa)
- 28s ribosomal protein s18c, mitochondrial isoform 1 (16 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- 39s ribosomal protein l18, mitochondrial isoform 1 (20 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l58 (23 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l21, mitochondrial isoform d (23 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l35, mitochondrial (21 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l28, mitochondrial (30 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l51, mitochondrial (15 kDa, Protein from Sus scrofa)
- Bl32m (21 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s23 (21 kDa, Protein from Sus scrofa)
- Guanosine-5'-monophosphate (363 Da, Ligand)
- Interferon alpha-inducible protein 6 (19 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s5, mitochondrial isoform x2 (48 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l52, mitochondrial (13 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s15, mitochondrial (27 kDa, Protein from Sus scrofa)
- Ul14m (15 kDa, Protein from Sus scrofa)
- Spermine (202 Da, Ligand)
- 39s ribosomal protein l50, mitochondrial (22 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l59, mitochondrial (25 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l9, mitochondrial (30 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l24, mitochondrial isoform x1 (24 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Sus scrofa)
- Ml42 (16 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s18a (22 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l48, mitochondrial (29 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s34 (25 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s11 (20 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s26, mitochondrial (23 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l37, mitochondrial (47 kDa, Protein from Sus scrofa)
- 55s mammalian mitochondrial ribosome with mtrrf (pre) and trna(p/e) (Complex)
- 39s ribosomal protein l19, mitochondrial (33 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l27, mitochondrial (15 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l34, mitochondrial (10 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l40 (24 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l45 (35 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l57 (12 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l30, mitochondrial (18 kDa, Protein from Sus scrofa)
- Ict1 (43 kDa, Protein from Sus scrofa)
- Cp trnaphe (23 kDa, RNA from Sus scrofa)
- Tgs domain-containing protein (38 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l13, mitochondrial (20 kDa, Protein from Sus scrofa)
- Mitoribosomal protein us12m, mrps12 (15 kDa, Protein from Sus scrofa)
- 12s rrna (308 kDa, RNA from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- 39s ribosomal protein l46, mitochondrial (32 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l44, mitochondrial (37 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l55 (15 kDa, Protein from Sus scrofa)
- Ribosomal_l2_c domain-containing protein (33 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s2, mitochondrial (31 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s35, mitochondrial isoform 1 (37 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s6 (30 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Sus scrofa)
- Coiled-coil-helix-coiled-coil-helix domain containing 1 (13 kDa, Protein from Sus scrofa)
- Ribosomal protein (10 kDa, Protein from Sus scrofa)
- Us17m (14 kDa, Protein from Sus scrofa)
- 55s mammalian mitochondrial ribosome (Complex from Sus scrofa)
- Aurora kinase a interacting protein 1 (22 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l16, mitochondrial (28 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l22, mitochondrial (24 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Mitochondrial ribosomal protein s33 (12 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l41 (15 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l54, mitochondrial (15 kDa, Protein from Sus scrofa)
- Unknown (1 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s22 (43 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Sus scrofa)
- Ribosome-recycling factor, mitochondrial (Complex from Homo sapiens)
- Mitochondrial ribosomal protein l47 (30 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l11, mitochondrial isoform a (20 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l12 (21 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l17, mitochondrial (19 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s28, mitochondrial (21 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l20, mitochondrial isoform 1 (17 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l4 (33 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l23, mitochondrial (17 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l38, mitochondrial (44 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l49, mitochondrial (18 kDa, Protein from Sus scrofa)
Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7o81
Q-score: 0.447
Bhatt PR, Scaiola A, Loughran G, Leibundgut M, Kratzel A, Meurs R, Dreos R, O'Connor KM, McMillan A, Bode JW, Thiel V, Gatfield D, Atkins JF, Ban N
Science (2021) 372 pp. 1306-1313 [ Pubmed: 34029205 DOI: doi:10.1126/science.abf3546 ]
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el13 (24 kDa, Protein from Oryctolagus cuniculus)
- Sars-cov-2 pseudoknot (Complex from Severe acute respiratory syndrome coronavirus 2)
- 60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s7 (47 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3a (30 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
- Water (18 Da, Ligand)
- Rabbit 80s ribosome colliding in another ribosome (Complex from Bos taurus)
- 40s ribosomal protein s18 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- Ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- 5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
- Ul29 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us11 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es21 (9 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el28 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul2 (28 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- Spermidine (145 Da, Ligand)
- Ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- El30 (12 kDa, Protein from Oryctolagus cuniculus)
- El24 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s9 (predicted) (22 kDa, Protein from Oryctolagus cuniculus)
- El33 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es4 (29 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul30 (29 kDa, Protein from Oryctolagus cuniculus)
- Replicase polyprotein 1ab (121 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es19 (16 kDa, Protein from Oryctolagus cuniculus)
- Edf1 (16 kDa, Protein from Oryctolagus cuniculus)
- Rabbit 80s ribosome colliding in another ribosome stalled by the sars-cov-2 pseudoknot (Complex)
- 40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el22 (14 kDa, Protein from Oryctolagus cuniculus)
- P-site trna(pro) (24 kDa, RNA from Bos taurus)
- 40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
- El39 (6 kDa, Protein from Oryctolagus cuniculus)
- Us15 (17 kDa, Protein from Oryctolagus cuniculus)
- Replicase polyprotein 1ab (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ribosomal protein es26 (13 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (28 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s27a (18 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- El43 (10 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s5 (22 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- Unknown atom or ion (Ligand)
- 40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- Rabbit 80s ribosome colliding in another ribosome (Complex from Oryctolagus cuniculus)
- Ribosomal protein es10 (18 kDa, Protein from Oryctolagus cuniculus)
- Us14 (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- El31 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3 (31 kDa, Protein from Oryctolagus cuniculus)
- A-site met-trna(met) (24 kDa, RNA from Bos taurus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Us9 (19 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
- El21 (18 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein us5 (31 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul1 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el8 (30 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- 28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
- El32 (15 kDa, Protein from Oryctolagus cuniculus)
- Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l40 (14 kDa, Protein from Oryctolagus cuniculus)
- Mrna containing sars-cov-2 sequence (69 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Ul23 (17 kDa, Protein from Oryctolagus cuniculus)
- El38 (8 kDa, Protein from Oryctolagus cuniculus)
- 18s rrna (603 kDa, RNA from Oryctolagus cuniculus)