Terminating ribosome with SRI-41315
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8scb
Q-score: 0.589
Coelho JPL, Yip MCJ, Oltion K, Taunton J, Shao S
Nat Chem Biol (2024) 20 pp. 877-884 [ DOI: doi:10.1038/s41589-023-01521-0 Pubmed: 38172604 ]
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
- 5.8s_rrna (50 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l7 (29 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
- Us12 (15 kDa, Protein from Oryctolagus cuniculus)
- Water (18 Da, Ligand)
- Es6 (28 kDa, Protein from Oryctolagus cuniculus)
- Us11 (18 kDa, Protein from Oryctolagus cuniculus)
- El23 (17 kDa, Protein from Oryctolagus cuniculus)
- Es19 (16 kDa, Protein from Oryctolagus cuniculus)
- Us10 (13 kDa, Protein from Oryctolagus cuniculus)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- Es27 (9 kDa, Protein from Oryctolagus cuniculus)
- Eukaryotic peptide chain release factor subunit 1 (51 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- E_trna (24 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- Es8 (24 kDa, Protein from Oryctolagus cuniculus)
- Us4 (22 kDa, Protein from Oryctolagus cuniculus)
- El22 (14 kDa, Protein from Oryctolagus cuniculus)
- Es12 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- S10_plectin domain-containing protein (18 kDa, Protein from Oryctolagus cuniculus)
- Us13 (17 kDa, Protein from Oryctolagus cuniculus)
- Nc (13 kDa, Protein from Homo sapiens)
- El13 (24 kDa, Protein from Oryctolagus cuniculus)
- Mrna (63 kDa, RNA from Homo sapiens)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Es25 (13 kDa, Protein from Oryctolagus cuniculus)
- El30 (12 kDa, Protein from Oryctolagus cuniculus)
- El41 (3 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l7a (36 kDa, Protein from Oryctolagus cuniculus)
- Us9 (16 kDa, Protein from Oryctolagus cuniculus)
- Receptor for activated c kinase 1 (rack1) (35 kDa, Protein from Oryctolagus cuniculus)
- El33 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s26 (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
- Es1 (30 kDa, Protein from Oryctolagus cuniculus)
- Es17 (15 kDa, Protein from Oryctolagus cuniculus)
- Es7 (22 kDa, Protein from Oryctolagus cuniculus)
- El20 (20 kDa, Protein from Oryctolagus cuniculus)
- Us19 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- P_trna (24 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
- El39 (6 kDa, Protein from Oryctolagus cuniculus)
- Us15 (17 kDa, Protein from Oryctolagus cuniculus)
- Atp binding cassette subfamily e member 1 (67 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- Us5 (31 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- El43 (10 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- 28s_rrna (1 MDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- El35 (14 kDa, Protein from Oryctolagus cuniculus)
- Us17 (18 kDa, Protein from Oryctolagus cuniculus)
- Us14 (6 kDa, Protein from Oryctolagus cuniculus)
- Terminating rabbit ribosome (4 MDa, Complex from Oryctolagus cuniculus)
- Ribosomal protein s3 (26 kDa, Protein from Oryctolagus cuniculus)
- El31 (14 kDa, Protein from Oryctolagus cuniculus)
- Us7 (22 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- Es30 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Us8 (14 kDa, Protein from Oryctolagus cuniculus)
- Es31 (18 kDa, Protein from Oryctolagus cuniculus)
- Es28 (7 kDa, Protein from Oryctolagus cuniculus)
- (2s,4as)-2-cyclobutyl-10-methyl-3-phenyl-2,10-dihydropyrimido[4,5-b]quinoline-4,5(3h,4ah)-dione (359 Da, Ligand)
- Us2 (sa) (32 kDa, Protein from Oryctolagus cuniculus)
- El21 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
- Es21 (9 kDa, Protein from Oryctolagus cuniculus)
- Ul24 (17 kDa, Protein from Oryctolagus cuniculus)
- 5s_rrna (38 kDa, RNA from Oryctolagus cuniculus)
- 18s_rrna (603 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin a-52 residue ribosomal protein fusion product 1 (10 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
- El32 (15 kDa, Protein from Oryctolagus cuniculus)
- El28 (15 kDa, Protein from Oryctolagus cuniculus)
- Es4 (s4 x isoform) (29 kDa, Protein from Oryctolagus cuniculus)
- Ul13 (23 kDa, Protein from Oryctolagus cuniculus)
- Iron/sulfur cluster (351 Da, Ligand)
Complex of UBE2O with NAP1L1 and ubiquitylated uL2
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7un3
Q-score: 0.334
Nat Struct Mol Biol (2022) 29 pp. 774-780 [ DOI: doi:10.1038/s41594-022-00807-6 Pubmed: 35915257 ]
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7un6
Q-score: 0.362
Nat Struct Mol Biol (2022) 29 pp. 774-780 [ DOI: doi:10.1038/s41594-022-00807-6 Pubmed: 35915257 ]
- (e3-independent) e2 ubiquitin-conjugating enzyme (147 kDa, Protein from Homo sapiens)
- Nucleosome assembly protein 1-like 1 (48 kDa, Protein from Homo sapiens)
- Complex of ube2o with nap1l1 (Complex from Homo sapiens)
SfSTING with c-di-GMP single fiber
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7un8
Q-score: 0.487
Morehouse BR, Yip MCJ, Keszei AFA, McNamara-Bordewick NK, Shao S, Kranzusch PJ
Nature (2022) 608 pp. 803-807 [ Pubmed: 35859168 DOI: doi:10.1038/s41586-022-04999-1 ]
- 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2h,7h-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6h-purin-6-one) (690 Da, Ligand)
- Cd-ntase-associated protein 12 (36 kDa, Protein from Sphingobacterium faecium)
- Sfsting with c-di-gmp single fiber (Complex from Sphingobacterium faecium)
SfSTING with c-di-GMP double fiber
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7un9
Q-score: 0.515
Morehouse BR, Yip MCJ, Keszei AFA, McNamara-Bordewick NK, Shao S, Kranzusch PJ
Nature (2022) 608 pp. 803-807 [ Pubmed: 35859168 DOI: doi:10.1038/s41586-022-04999-1 ]
- Sfsting with c-di-gmp double fiber (Complex from Sphingobacterium faecium)
- 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2h,7h-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6h-purin-6-one) (690 Da, Ligand)
- Cd-ntase-associated protein 12 (34 kDa, Protein from Sphingobacterium faecium)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7una
Q-score: 0.415
Morehouse BR, Yip MCJ, Keszei AFA, McNamara-Bordewick NK, Shao S, Kranzusch PJ
Nature (2022) 608 pp. 803-807 [ Pubmed: 35859168 DOI: doi:10.1038/s41586-022-04999-1 ]
- Cd-ntase-associated protein 12 (36 kDa, Protein from Sphingobacterium faecium)
- 2-amino-9-[(2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-9-(6-amino-9h-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2h,7h-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6h-purin-6-one (674 Da, Ligand)
- Sfsting with cgamp (Complex from Sphingobacterium faecium)
Metazoan pre-targeting GET complex (cBUGG-in)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7ru9
Q-score: 0.423
Keszei AFA, Yip MCJ, Hsieh TC, Shao S
Nat Struct Mol Biol (2021) 28 pp. 1029-1037 [ Pubmed: 34887561 DOI: doi:10.1038/s41594-021-00690-7 ]
- Zinc ion (65 Da, Ligand)
- Large proline-rich protein bag6 (14 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atpase get3 (38 kDa, Protein from Danio rerio)
- Golgi to er traffic protein 4 homolog (37 kDa, Protein from Homo sapiens)
- Metazoan pre-targeting get complex cbugg-in (Complex from Danio rerio)
- Ubiquitin-like protein 4a (18 kDa, Protein from Homo sapiens)
Metazoan pre-targeting GET complex (cBUGG-out)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7rua
Q-score: 0.409
Keszei AFA, Yip MCJ, Hsieh TC, Shao S
Nat Struct Mol Biol (2021) 28 pp. 1029-1037 [ Pubmed: 34887561 DOI: doi:10.1038/s41594-021-00690-7 ]
- Zinc ion (65 Da, Ligand)
- Metazoan pre-targeting get complex cbugg-out (Complex from Danio rerio)
- Large proline-rich protein bag6 (14 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atpase get3 (38 kDa, Protein from Danio rerio)
- Golgi to er traffic protein 4 homolog (37 kDa, Protein from Homo sapiens)
- Ubiquitin-like protein 4a (18 kDa, Protein from Homo sapiens)
Metazoan pre-targeting GET complex with SGTA (cBUGGS)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7ruc
Q-score: 0.424
Keszei AFA, Yip MCJ, Hsieh TC, Shao S
Nat Struct Mol Biol (2021) 28 pp. 1029-1037 [ Pubmed: 34887561 DOI: doi:10.1038/s41594-021-00690-7 ]
- Zinc ion (65 Da, Ligand)
- Large proline-rich protein bag6 (14 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Atpase get3 (38 kDa, Protein from Danio rerio)
- Golgi to er traffic protein 4 homolog (37 kDa, Protein from Homo sapiens)
- Metazoan pre-targeting get complex with sgta (Complex from Danio rerio)
- Ubiquitin-like protein 4a (18 kDa, Protein from Homo sapiens)
80S rabbit ribosome stalled with benzamide-CHX
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7mdz
Q-score: 0.502
Koga Y, Hoang EM, Park Y, Keszei AFA, Murray J, Shao S, Liau BB
J Am Chem Soc (2021) 143 pp. 13473-13477 [ Pubmed: 34403584 DOI: doi:10.1021/jacs.1c05146 ]
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- Ul3 (46 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l7 (29 kDa, Protein from Oryctolagus cuniculus)
- Us12 (15 kDa, Protein from Oryctolagus cuniculus)
- Es6 (28 kDa, Protein from Oryctolagus cuniculus)
- Us11 (18 kDa, Protein from Oryctolagus cuniculus)
- 80s rabbit ribosome stalled with benzamide-chx (4 MDa, Complex from Oryctolagus cuniculus)
- 18s rrna (602 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- El23 (17 kDa, Protein from Oryctolagus cuniculus)
- Es19 (16 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- Us10 (13 kDa, Protein from Oryctolagus cuniculus)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- Es27 (9 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- Ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- Es8 (24 kDa, Protein from Oryctolagus cuniculus)
- Us4 (22 kDa, Protein from Oryctolagus cuniculus)
- El22 (14 kDa, Protein from Oryctolagus cuniculus)
- Es12 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- S10_plectin domain-containing protein (18 kDa, Protein from Oryctolagus cuniculus)
- Us13 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Es25 (13 kDa, Protein from Oryctolagus cuniculus)
- El30 (12 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (47 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l7a (36 kDa, Protein from Oryctolagus cuniculus)
- Us9 (16 kDa, Protein from Oryctolagus cuniculus)
- El33 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s26 (13 kDa, Protein from Oryctolagus cuniculus)
- 5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
- Es1 (30 kDa, Protein from Oryctolagus cuniculus)
- Es17 (15 kDa, Protein from Oryctolagus cuniculus)
- Es29 (6 kDa, Protein from Oryctolagus cuniculus)
- Es7 (22 kDa, Protein from Oryctolagus cuniculus)
- Us19 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
- El39 (6 kDa, Protein from Oryctolagus cuniculus)
- Us15 (17 kDa, Protein from Oryctolagus cuniculus)
- El40 (11 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- Mrna (3 kDa, RNA from synthetic construct)
- Us5 (31 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- El43 (10 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- 28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
- P-site trna (24 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- El35 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
- Us17 (18 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s3 (26 kDa, Protein from Oryctolagus cuniculus)
- El31 (14 kDa, Protein from Oryctolagus cuniculus)
- Us7 (22 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- Es30 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Us8 (14 kDa, Protein from Oryctolagus cuniculus)
- Es31 (18 kDa, Protein from Oryctolagus cuniculus)
- Es28 (7 kDa, Protein from Oryctolagus cuniculus)
- El21 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
- Ul24 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
- 5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
- El32 (15 kDa, Protein from Oryctolagus cuniculus)
- Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
- El28 (15 kDa, Protein from Oryctolagus cuniculus)
- N-[(1r,3s,4r,5s)-3-{(1r)-2-[(2r,4r,6s)-2,6-dihydroxypiperidin-4-yl]-1-hydroxyethyl}-4-hydroxy-1,5-dimethylcyclohexyl]benzamide (400 Da, Ligand)
- Ul13 (23 kDa, Protein from Oryctolagus cuniculus)