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 [ Pubmed: 37347872 DOI: doi:10.1126/science.adg3297 ]
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- Es26 (13 kDa, Protein from Oryctolagus cuniculus)
- 5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l22 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- Ribosome translating a cytosolic peptide (Complex from Homo sapiens)
- Complex of nac and metap1 at the tennel exit of translating ribosome (Complex)
- 40s ribosomal protein s7 (47 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
- Nascent polypeptide-associated complex subunit alpha (23 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
- Acetylamino-acetic acid (117 Da, Ligand)
- 40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l31 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l5 eukaryotic c-terminal domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3 (31 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s5 (22 kDa, Protein from Oryctolagus cuniculus)
- 5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l39-like (6 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l23en domain-containing protein (17 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (28 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
- Methionine aminopeptidase 1 (43 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l28 (15 kDa, Protein from Oryctolagus cuniculus)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Water (18 Da, Ligand)
- 60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s19 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Ternary complex of translating ribosome, nac and metap1 (Complex from Oryctolagus cuniculus)
- 60s ribosomal protein l7a (30 kDa, Protein from Oryctolagus cuniculus)
- 18s rrna (603 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
- 28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s14 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s27a (18 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
- S10_plectin domain-containing protein (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s18 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l32 (15 kDa, Protein from Oryctolagus cuniculus)
- Spermine (202 Da, Ligand)
- Any 5'-monophosphate nucleotide (214 Da, Ligand)
- 40s ribosomal protein s3a (30 kDa, Protein from Oryctolagus cuniculus)
- Unknown atom or ion (Ligand)
- Ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
- E-site trna (15 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
- Spermidine (145 Da, Ligand)
- Us9 (19 kDa, Protein from Oryctolagus cuniculus)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s29 (6 kDa, Protein from Oryctolagus cuniculus)
- P-site val-trna (24 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s13 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l30 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul1 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul30 (29 kDa, Protein from Oryctolagus cuniculus)
- El18 (21 kDa, Protein from Oryctolagus cuniculus)
- Transcription factor btf3 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s9 (22 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
- Glucose-6-phosphate isomerase (7 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l37a (10 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
Structure of the TRAP complex with the Sec translocon and a translating ribosome
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8btk
Q-score: 0.362
Jaskolowski M, Jomaa A, Gamerdinger M, Shrestha S, Leibundgut M, Deuerling E, Ban N
Nat Struct Mol Biol (2023) 30 pp. 770-777 [ DOI: doi:10.1038/s41594-023-00990-0 Pubmed: 37170030 ]
- Ribosomal large subunit (60s) (Complex from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- Us15 (17 kDa, Protein from Oryctolagus cuniculus)
- Sec61 translocon (Complex from canis lupus familiaris)
- P-site trna (24 kDa, RNA from Oryctolagus cuniculus)
- P-site trna (Complex from Oryctolagus cuniculus)
- Ribosomal protein s9 (predicted) (22 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s19 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul1 (24 kDa, Protein from Oryctolagus cuniculus)
- Translocon-associated protein subunit delta (18 kDa, Protein from Canis lupus familiaris)
- El43 (10 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l28 (15 kDa, Protein from Oryctolagus cuniculus)
- El39 (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l22 (14 kDa, Protein from Oryctolagus cuniculus)
- El32 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3a (30 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l23en domain-containing protein (17 kDa, Protein from Oryctolagus cuniculus)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Canis lupus familiaris)
- 60s ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
- Us9 (19 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
- Spermidine (145 Da, Ligand)
- Ul30,60s ribosomal protein l7 (29 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- Trap complex (Complex from canis lupus familiaris)
- Zinc ion (65 Da, Ligand)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- Spermine (202 Da, Ligand)
- 40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s7 (47 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
- El18 (21 kDa, Protein from Oryctolagus cuniculus)
- L13 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal small subunit (ssu) (Complex from Oryctolagus cuniculus)
- Ubiquitin (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
- Structure of the trap complex with the sec translocon and a translating ribosome (Complex from Oryctolagus cuniculus)
- Ribosomal protein l31 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s27a (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l7a (30 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- 5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- Signal sequence receptor subunit 3 (21 kDa, Protein from Canis lupus familiaris)
- Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
- Nascent chain (2 kDa, Protein from Saccharomyces cerevisiae)
- Acetylamino-acetic acid (117 Da, Ligand)
- 40s ribosomal protein s18 (17 kDa, Protein from Oryctolagus cuniculus)
- 28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s14 (16 kDa, Protein from Oryctolagus cuniculus)
- El30 (12 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Canis lupus familiaris)
- Ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Canis lupus familiaris)
- 18s rrna (603 kDa, RNA from Oryctolagus cuniculus)
- Ribosomal_s5_c domain-containing protein,40s ribosomal protein s2 (31 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (28 kDa, Protein from Oryctolagus cuniculus)
- Us14 (6 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
- Es26 (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- Mrna (1 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s5 (22 kDa, Protein from Oryctolagus cuniculus)
- Translocon-associated protein subunit alpha (32 kDa, Protein from Canis lupus familiaris)
- Translocon-associated protein subunit beta (20 kDa, Protein from Canis lupus familiaris)
- El38 (8 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es10 (18 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3 (31 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- 5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6frk
Q-score: 0.363
Kobayashi K, Jomaa A, Lee JH, Chandrasekar S, Boehringer D, Shan SO, Ban N
Science (2018) 360 pp. 323-327 [ Pubmed: 29567807 DOI: doi:10.1126/science.aar7924 ]
- Ribosomal protein el34 (12 kDa, Protein from Rabbit)
- Ribosomal protein el41 (3 kDa, Protein from Rabbit)
- Ribosomal protein ul5 (19 kDa, Protein from Rabbit)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Signal recognition particle subunit srp72,signal recognition particle subunit srp72,signal recognition particle subunit srp72 (67 kDa, Protein from Dog)
- Ribosomal protein el43 (10 kDa, Protein from Rabbit)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- Ribosomal protein el21 (18 kDa, Protein from Rabbit)
- Ribosomal protein el13 (24 kDa, Protein from Rabbit)
- Ribosomal protein ul13 (23 kDa, Protein from Rabbit)
- Srp (Complex from Canis lupus familiaris)
- Ribosomal protein el38 (8 kDa, Protein from Rabbit)
- Signal recognition particle subunit srp19 (12 kDa, Protein from Dog)
- Ribosome (Complex from Oryctolagus cuniculus)
- Ribosomal protein el42 (12 kDa, Protein from Rabbit)
- Signal recognition particle 14 kda protein (12 kDa, Protein from Dog)
- Ribosomal protein ul24 (15 kDa, Protein from Rabbit)
- Canis lupus familiaris rna, 7sl, cytoplasmic 1 (rn7sl1), srp rna (96 kDa, RNA from Canis lupus familiaris)
- Ribosomal protein ul18 (33 kDa, Protein from Rabbit)
- Ribosomal protein el30 (10 kDa, Protein from Rabbit)
- Ribosomal protein el6 (27 kDa, Protein from Rabbit)
- Ribosomal protein l12 (17 kDa, Protein from Rabbit)
- 5.8s ribosomal rna (50 kDa, RNA from Rabbit)
- Ribosomal protein el31 (12 kDa, Protein from Rabbit)
- Ribosomal protein ul4 (41 kDa, Protein from Rabbit)
- Ribosomal protein el20 (20 kDa, Protein from Rabbit)
- Ribosomal protein ul6 (21 kDa, Protein from Rabbit)
- Ribosomal protein ul30 (26 kDa, Protein from Rabbit)
- Ribosomal protein el14 (16 kDa, Protein from Rabbit)
- Signal sequence (Complex from Saccharomyces cerevisiae)
- Signal recognition particle subunit srp68 (65 kDa, Protein from Dog)
- Translating ribosome bound to srp and srp receptor (Complex)
- Ribosomal protein el18 (21 kDa, Protein from Rabbit)
- 60s ribosomal protein l27 (15 kDa, Protein from Rabbit)
- Ribosomal protein el32 (15 kDa, Protein from Rabbit)
- Ribosomal protein el22 (11 kDa, Protein from Rabbit)
- Ribosomal protein l8 (26 kDa, Protein from Rabbit)
- Ribosomal protein ul22 (17 kDa, Protein from Rabbit)
- Ribosomal protein el36 (11 kDa, Protein from Rabbit)
- Ribosomal protein ul23 (13 kDa, Protein from Rabbit)
- Signal sequence (1 kDa, Protein from Saccharomyces cerevisiae)
- Ribosomal protein el8 (27 kDa, Protein from Rabbit)
- Ribosomal protein ul3 (44 kDa, Protein from Rabbit)
- 5s ribosomal rna (38 kDa, RNA from Rabbit)
- Ribosomal protein l23 (13 kDa, Protein from Rabbit)
- 60s ribosomal protein l29 (8 kDa, Protein from Rabbit)
- Srp receptor beta subunit (23 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el28 (14 kDa, Protein from Rabbit)
- Ribosomal protein ul16 (24 kDa, Protein from Rabbit)
- Signal recognition particle 54 kda protein (55 kDa, Protein from Dog)
- Trna (24 kDa, RNA from Rabbit)
- Ribosomal protein ul29 (14 kDa, Protein from Rabbit)
- Ribosomal protein el39 (6 kDa, Protein from Rabbit)
- Signal recognition particle 9 kda protein (8 kDa, Protein from Dog)
- Ribosomal protein el33 (12 kDa, Protein from Rabbit)
- 28s ribosomal rna (1 MDa, RNA from Rabbit)
- Ribosomal protein l37 (10 kDa, Protein from Rabbit)
- Zinc ion (65 Da, Ligand)
- Ribosomal protein el40 (6 kDa, Protein from Rabbit)
- Ribosomal protein el24 (7 kDa, Protein from Rabbit)
- Srp receptor (Complex from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (22 kDa, Protein from Rabbit)
- Magnesium ion (24 Da, Ligand)
- Ribosomal protein ul15 (16 kDa, Protein from Rabbit)
- Ribosomal protein l15 (24 kDa, Protein from Rabbit)
- Srp receptor alpha subunit (72 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el19 (21 kDa, Protein from Rabbit)