Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8bhf
Q-score: 0.492
Gangwar SP, Yen LY, Yelshanskaya MV, Korman A, Jones DR, Sobolevsky AI
Nat Struct Mol Biol (2023) 30 pp. 1481-1494 [ DOI: doi:10.1038/s41594-023-01080-x Pubmed: 37653241 ]
- 60s ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l6 (28 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l10a (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s15 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin-60s ribosomal protein l40 (6 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s16 (16 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s7 (21 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l26 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l31 (12 kDa, Protein from Oryctolagus cuniculus)
- 5.8s ribosomal rna (50 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- 18s ribosomal rna (547 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l7 (26 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (10 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s20 (11 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s17 (15 kDa, Protein from Oryctolagus cuniculus)
- 28s ribosomal rna (1 MDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein s14 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (21 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l14 (16 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l19 (21 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l7a (27 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l37a (10 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l28 (14 kDa, Protein from Oryctolagus cuniculus)
- Mrna (896 Da, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (13 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s26 (11 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l17 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3a (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin-40s ribosomal protein s27a (7 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (11 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s3 (25 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosome complex (Complex from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (41 kDa, Protein from Oryctolagus cuniculus)
- 5s ribosomal rna (38 kDa, RNA from Oryctolagus cuniculus)
- 40s_sa_c domain-containing protein (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l22 (11 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l30 (10 kDa, Protein from Oryctolagus cuniculus)
- P-site trna (24 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l5 (34 kDa, Protein from Oryctolagus cuniculus)
- Plectin/s10 n-terminal domain-containing protein (11 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s9 (predicted) (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l8 (26 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (27 kDa, Protein from Oryctolagus cuniculus)
- Ccr4-not transcription complex subunit 3 (28 kDa, Protein from Homo sapiens)
- Ribosomal protein s5 (21 kDa, Protein from Oryctolagus cuniculus)
- Trash domain-containing protein (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein rack1 (34 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s2 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l32 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l36a like (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s25 (8 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (45 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein us15 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s18 (16 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s19 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l39-like (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l11 (19 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin-like domain-containing protein (6 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23/l25 n-terminal domain-containing protein (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l12 (16 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s29 (6 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- Nascent chain (501 Da, Protein from Oryctolagus cuniculus)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7o9k
Q-score: 0.428
Cipullo M, Gese GV, Khawaja A, Hallberg BM, Rorbach J
Nat Commun (2021) 12 pp. 3673-3673 [ Pubmed: 34135318 DOI: doi:10.1038/s41467-021-23617-8 ]
- Mitochondrial ribosome-associated gtpase 1 (37 kDa, Protein from Human)
- 39s ribosomal protein l54, mitochondrial (15 kDa, Protein from Human)
- 55s subunit assembly intermediate (1 MDa, Complex from Homo sapiens)
- 16s rrna (500 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l33, mitochondrial (7 kDa, Protein from Human)
- Rrna methyltransferase 2, mitochondrial (27 kDa, Protein from Human)
- 39s ribosomal protein l43, mitochondrial (23 kDa, Protein from Human)
- 39s ribosomal protein l2, mitochondrial (33 kDa, Protein from Human)
- 39s ribosomal protein l41, mitochondrial (15 kDa, Protein from Human)
- 39s ribosomal protein l55, mitochondrial (15 kDa, Protein from Human)
- Mief1 upstream open reading frame protein (8 kDa, Protein from Human)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 39s ribosomal protein l52, mitochondrial (13 kDa, Protein from Human)
- 39s ribosomal protein l35, mitochondrial (21 kDa, Protein from Human)
- 39s ribosomal protein l3, mitochondrial (38 kDa, Protein from Human)
- 39s ribosomal protein l17, mitochondrial (20 kDa, Protein from Human)
- 39s ribosomal protein l40, mitochondrial (24 kDa, Protein from Human)
- 39s ribosomal protein l30, mitochondrial (18 kDa, Protein from Human)
- 39s ribosomal protein l15, mitochondrial (33 kDa, Protein from Human)
- 39s ribosomal protein l28, mitochondrial (30 kDa, Protein from Human)
- 39s ribosomal protein l34, mitochondrial (10 kDa, Protein from Human)
- 39s ribosomal protein l51, mitochondrial (15 kDa, Protein from Human)
- 39s ribosomal protein l16, mitochondrial (28 kDa, Protein from Human)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 39s ribosomal protein l10, mitochondrial (29 kDa, Protein from Human)
- 5-methylcytosine rrna methyltransferase nsun4 (43 kDa, Protein from Human)
- 39s ribosomal protein l13, mitochondrial (20 kDa, Protein from Human)
- 39s ribosomal protein l42, mitochondrial (16 kDa, Protein from Human)
- 39s ribosomal protein l20, mitochondrial (17 kDa, Protein from Human)
- 39s ribosomal protein l45, mitochondrial (35 kDa, Protein from Human)
- Mitochondrial assembly of ribosomal large subunit protein 1 (26 kDa, Protein from Human)
- Growth arrest and dna damage-inducible proteins-interacting protein 1 (25 kDa, Protein from Human)
- 39s ribosomal protein l36, mitochondrial (11 kDa, Protein from Human)
- Unk (2 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l9, mitochondrial (30 kDa, Protein from Human)
- 39s ribosomal protein l46, mitochondrial (31 kDa, Protein from Human)
- 39s ribosomal protein s30, mitochondrial (50 kDa, Protein from Human)
- 39s ribosomal protein l12, mitochondrial (21 kDa, Protein from Human)
- 39s ribosomal protein l37, mitochondrial (48 kDa, Protein from Human)
- Mt-trnaval (22 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l23, mitochondrial (17 kDa, Protein from Human)
- 39s ribosomal protein l24, mitochondrial (24 kDa, Protein from Human)
- 39s ribosomal protein l49, mitochondrial (19 kDa, Protein from Human)
- 39s ribosomal protein l47, mitochondrial (29 kDa, Protein from Human)
- Elongation factor tu, mitochondrial (49 kDa, Protein from Human)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Mitochondrial ribosome-associated gtpase 2 (45 kDa, Protein from Homo sapiens)
- Transcription termination factor 4, mitochondrial (44 kDa, Protein from Human)
- 39s ribosomal protein l4, mitochondrial (34 kDa, Protein from Human)
- 39s ribosomal protein l14, mitochondrial (15 kDa, Protein from Human)
- 39s ribosomal protein l48, mitochondrial (23 kDa, Protein from Human)
- Ribosomal protein 63, mitochondrial (12 kDa, Protein from Human)
- S-adenosylmethionine (398 Da, Ligand)
- 39s ribosomal protein l19, mitochondrial (33 kDa, Protein from Human)
- Mitochondrial ribosomal protein l18, isoform cra_b (20 kDa, Protein from Human)
- 39s ribosomal protein l11, mitochondrial (20 kDa, Protein from Human)
- 39s ribosomal protein l44, mitochondrial (37 kDa, Protein from Human)
- 39s ribosomal protein l32, mitochondrial (21 kDa, Protein from Human)
- 39s ribosomal protein l39, mitochondrial (38 kDa, Protein from Human)
- 39s ribosomal protein l38, mitochondrial (44 kDa, Protein from Human)
- 39s ribosomal protein l53, mitochondrial (12 kDa, Protein from Human)
- Peptidyl-trna hydrolase ict1, mitochondrial (23 kDa, Protein from Human)
- 39s ribosomal protein l27, mitochondrial (16 kDa, Protein from Human)
- 39s ribosomal protein l50, mitochondrial (18 kDa, Protein from Human)
- 39s ribosomal protein s18a, mitochondrial (22 kDa, Protein from Human)
- Acyl carrier protein, mitochondrial (17 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- 4'-phosphopantetheine (358 Da, Ligand)
- 39s ribosomal protein l22, mitochondrial (24 kDa, Protein from Human)
- 39s ribosomal protein l21, mitochondrial (22 kDa, Protein from Human)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7o9m
Q-score: 0.52
Cipullo M, Gese GV, Khawaja A, Hallberg BM, Rorbach J
Nat Commun (2021) 12 pp. 3673-3673 [ Pubmed: 34135318 DOI: doi:10.1038/s41467-021-23617-8 ]
- Peptidyl-trna hydrolase ict1, mitochondrial (23 kDa, Protein from Human)
- 39s ribosomal protein l54, mitochondrial (15 kDa, Protein from Human)
- 55s subunit assembly intermediate (1 MDa, Complex from Homo sapiens)
- 16s rrna (500 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l33, mitochondrial (7 kDa, Protein from Human)
- Rrna methyltransferase 2, mitochondrial (27 kDa, Protein from Human)
- 39s ribosomal protein l43, mitochondrial (23 kDa, Protein from Human)
- 39s ribosomal protein l2, mitochondrial (33 kDa, Protein from Human)
- 39s ribosomal protein l41, mitochondrial (15 kDa, Protein from Human)
- 39s ribosomal protein l55, mitochondrial (15 kDa, Protein from Human)
- Mief1 upstream open reading frame protein (8 kDa, Protein from Human)
- Unknown residues (2 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 39s ribosomal protein l52, mitochondrial (13 kDa, Protein from Human)
- 39s ribosomal protein l35, mitochondrial (21 kDa, Protein from Human)
- 39s ribosomal protein l3, mitochondrial (38 kDa, Protein from Human)
- 39s ribosomal protein l17, mitochondrial (20 kDa, Protein from Human)
- Mitochondrial ribosome-associated gtpase 1 (37 kDa, Protein from Human)
- 39s ribosomal protein l40, mitochondrial (24 kDa, Protein from Human)
- 39s ribosomal protein l30, mitochondrial (18 kDa, Protein from Human)
- 39s ribosomal protein l15, mitochondrial (33 kDa, Protein from Human)
- 39s ribosomal protein l28, mitochondrial (30 kDa, Protein from Human)
- 39s ribosomal protein l34, mitochondrial (10 kDa, Protein from Human)
- 39s ribosomal protein l51, mitochondrial (15 kDa, Protein from Human)
- 39s ribosomal protein l16, mitochondrial (28 kDa, Protein from Human)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 39s ribosomal protein l10, mitochondrial (29 kDa, Protein from Human)
- 5-methylcytosine rrna methyltransferase nsun4 (43 kDa, Protein from Human)
- 39s ribosomal protein l13, mitochondrial (20 kDa, Protein from Human)
- 39s ribosomal protein l20, mitochondrial (17 kDa, Protein from Human)
- 39s ribosomal protein l42, mitochondrial (16 kDa, Protein from Human)
- Mitochondrial assembly of ribosomal large subunit protein 1 (26 kDa, Protein from Human)
- Growth arrest and dna damage-inducible proteins-interacting protein 1 (25 kDa, Protein from Human)
- 39s ribosomal protein l36, mitochondrial (11 kDa, Protein from Human)
- 39s ribosomal protein l9, mitochondrial (30 kDa, Protein from Human)
- 39s ribosomal protein l46, mitochondrial (31 kDa, Protein from Human)
- 39s ribosomal protein s30, mitochondrial (50 kDa, Protein from Human)
- 39s ribosomal protein l23, mitochondrial (17 kDa, Protein from Human)
- Mt-trnaval (22 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l24, mitochondrial (24 kDa, Protein from Human)
- 39s ribosomal protein l37, mitochondrial (48 kDa, Protein from Human)
- 39s ribosomal protein l12, mitochondrial (21 kDa, Protein from Human)
- 39s ribosomal protein l49, mitochondrial (19 kDa, Protein from Human)
- 39s ribosomal protein l47, mitochondrial (29 kDa, Protein from Human)
- 39s ribosomal protein l14, mitochondrial (15 kDa, Protein from Human)
- 39s ribosomal protein l4, mitochondrial (34 kDa, Protein from Human)
- 39s ribosomal protein l48, mitochondrial (23 kDa, Protein from Human)
- Ribosomal protein 63, mitochondrial (12 kDa, Protein from Human)
- Transcription termination factor 4, mitochondrial (44 kDa, Protein from Human)
- S-adenosylmethionine (398 Da, Ligand)
- 39s ribosomal protein l19, mitochondrial (33 kDa, Protein from Human)
- Mitochondrial ribosomal protein l18, isoform cra_b (20 kDa, Protein from Human)
- 39s ribosomal protein l45, mitochondrial (34 kDa, Protein from Human)
- 39s ribosomal protein l11, mitochondrial (20 kDa, Protein from Human)
- 39s ribosomal protein l44, mitochondrial (37 kDa, Protein from Human)
- 39s ribosomal protein l32, mitochondrial (21 kDa, Protein from Human)
- 39s ribosomal protein l39, mitochondrial (38 kDa, Protein from Human)
- 39s ribosomal protein l38, mitochondrial (44 kDa, Protein from Human)
- 39s ribosomal protein l53, mitochondrial (12 kDa, Protein from Human)
- Acyl carrier protein, mitochondrial (17 kDa, Protein from Human)
- 39s ribosomal protein l27, mitochondrial (16 kDa, Protein from Human)
- 39s ribosomal protein l50, mitochondrial (18 kDa, Protein from Human)
- 39s ribosomal protein s18a, mitochondrial (22 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- 4'-phosphopantetheine (358 Da, Ligand)
- 39s ribosomal protein l22, mitochondrial (24 kDa, Protein from Human)
- 39s ribosomal protein l21, mitochondrial (22 kDa, Protein from Human)