Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolution
Resolution: 2.63 Å
EM Method: Single-particle
Fitted PDBs: 7qi5
Q-score: 0.594
Singh V, Itoh Y, Del'Olio S, Hassan A, Naschberger A, Flygaard RK, Nobe Y, Izumikawa K, Aibara S, Andrell J, Whitford PC, Barrientos A, Taoka M, Amunts A
bioRxiv (2023) [ DOI: doi:10.1101/2023.05.24.542018 Pubmed: 37503168 ]
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Spermidine (145 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 39s ribosomal protein l17, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- 1,4-diaminobutane (88 Da, Ligand)
- 39s ribosomal protein l47, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l37, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l54, mitochondrial (15 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 16s mitochondrial rrna (500 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l52, mitochondrial (13 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l4, mitochondrial (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 39s ribosomal protein l35, mitochondrial (21 kDa, Protein from Homo sapiens)
- Mrna (10 kDa, RNA from Homo sapiens)
- 39s ribosomal protein s30, mitochondrial (50 kDa, Protein from Homo sapiens)
- Ribosomal protein 63, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l20, mitochondrial (17 kDa, Protein from Homo sapiens)
- P/p-trna (22 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l30, mitochondrial (18 kDa, Protein from Homo sapiens)
- E/e-trna (22 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l43, mitochondrial (23 kDa, Protein from Homo sapiens)
- Spermine (202 Da, Ligand)
- 39s ribosomal protein l49, mitochondrial (19 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l2, mitochondrial (33 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l39, mitochondrial (38 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l40, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l53, mitochondrial (12 kDa, Protein from Homo sapiens)
- Peptidyl-trna hydrolase ict1, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l13, mitochondrial (20 kDa, Protein from Homo sapiens)
- A/a-trna (21 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l18, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l41, mitochondrial (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 39s ribosomal protein s18a, mitochondrial (22 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l11, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l21, mitochondrial (22 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l23, mitochondrial (17 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l46, mitochondrial (31 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l12, mitochondrial (21 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l42, mitochondrial (16 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l9, mitochondrial (30 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l32, mitochondrial (21 kDa, Protein from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l44, mitochondrial (37 kDa, Protein from Homo sapiens)
- Valine (117 Da, Ligand)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l48, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 39s ribosomal protein l36, mitochondrial (11 kDa, Protein from Homo sapiens)
- Human mitochondrial ribosome (Complex from Homo sapiens)
- 39s ribosomal protein l3, mitochondrial (38 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l27, mitochondrial (16 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l22, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l51, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l50, mitochondrial (18 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l1, mitochondrial (36 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l15, mitochondrial (33 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l33, mitochondrial (7 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l16, mitochondrial (28 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l19, mitochondrial (33 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l28, mitochondrial (30 kDa, Protein from Homo sapiens)
- Mitochondrial trnaval (22 kDa, RNA from Homo sapiens)
- Mrps21 isoform 1 (10 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l24, mitochondrial (24 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l38, mitochondrial (44 kDa, Protein from Homo sapiens)
- Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (13 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l55, mitochondrial (15 kDa, Protein from Homo sapiens)
- Growth arrest and dna damage-inducible proteins-interacting protein 1 (25 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l34, mitochondrial (10 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l45, mitochondrial (35 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l10, mitochondrial (29 kDa, Protein from Homo sapiens)
Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolution
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 7qi6
Q-score: 0.539
Singh V, Itoh Y, Del'Olio S, Hassan A, Naschberger A, Flygaard RK, Nobe Y, Izumikawa K, Aibara S, Andrell J, Whitford PC, Barrientos A, Taoka M, Amunts A
bioRxiv (2023) [ DOI: doi:10.1101/2023.05.24.542018 Pubmed: 37503168 ]
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Spermidine (145 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 39s ribosomal protein l17, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- 1,4-diaminobutane (88 Da, Ligand)
- 39s ribosomal protein l47, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l37, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l54, mitochondrial (15 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 16s mitochondrial rrna (500 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l52, mitochondrial (13 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l4, mitochondrial (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 39s ribosomal protein l35, mitochondrial (21 kDa, Protein from Homo sapiens)
- 39s ribosomal protein s30, mitochondrial (50 kDa, Protein from Homo sapiens)
- Ribosomal protein 63, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l20, mitochondrial (17 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l30, mitochondrial (18 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l43, mitochondrial (23 kDa, Protein from Homo sapiens)
- Spermine (202 Da, Ligand)
- 39s ribosomal protein l49, mitochondrial (19 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l2, mitochondrial (33 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l39, mitochondrial (38 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l40, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l53, mitochondrial (12 kDa, Protein from Homo sapiens)
- Peptidyl-trna hydrolase ict1, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l13, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l18, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- P/e-trna (22 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Mrna (10 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l41, mitochondrial (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 39s ribosomal protein s18a, mitochondrial (22 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l11, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l21, mitochondrial (22 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l23, mitochondrial (17 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l46, mitochondrial (31 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l12, mitochondrial (21 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l42, mitochondrial (16 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l9, mitochondrial (30 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l32, mitochondrial (21 kDa, Protein from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l44, mitochondrial (37 kDa, Protein from Homo sapiens)
- Valine (117 Da, Ligand)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l48, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 39s ribosomal protein l36, mitochondrial (11 kDa, Protein from Homo sapiens)
- Human mitochondrial ribosome (Complex from Homo sapiens)
- 39s ribosomal protein l3, mitochondrial (38 kDa, Protein from Homo sapiens)
- A/p-trna (21 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l27, mitochondrial (16 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l22, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l51, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l50, mitochondrial (18 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l1, mitochondrial (36 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l15, mitochondrial (33 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l33, mitochondrial (7 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l16, mitochondrial (28 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l19, mitochondrial (33 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l28, mitochondrial (30 kDa, Protein from Homo sapiens)
- Mitochondrial trnaval (22 kDa, RNA from Homo sapiens)
- Mrps21 isoform 1 (10 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l24, mitochondrial (24 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l38, mitochondrial (44 kDa, Protein from Homo sapiens)
- Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (13 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l55, mitochondrial (15 kDa, Protein from Homo sapiens)
- Growth arrest and dna damage-inducible proteins-interacting protein 1 (25 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l34, mitochondrial (10 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l45, mitochondrial (35 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l10, mitochondrial (29 kDa, Protein from Homo sapiens)
Specific features and methylation sites of a plant 80S ribosome
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 7qiz
Q-score: 0.666
Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lison P, Taoka M, Amunts A
Plant Commun. (2022) 3 pp. 100342-100342 [ Pubmed: 35643637 DOI: doi:10.1016/j.xplc.2022.100342 ]
- Ribosomal protein l15 (24 kDa, Protein from Solanum lycopersicum)
- 5s rrna (38 kDa, RNA from Solanum lycopersicum)
- 40s ribosomal protein us14 (6 kDa, Protein from Solanum lycopersicum)
- Thaliana 60s ribosomal protein l7 (28 kDa, Protein from Solanum lycopersicum)
- Spermidine (145 Da, Ligand)
- 40s ribosomal protein s15a-1 (14 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l3 (44 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s17 (16 kDa, Protein from Solanum lycopersicum)
- 18s (583 kDa, RNA from Solanum lycopersicum)
- 1,4-diaminobutane (88 Da, Ligand)
- 60s ribosomal protein l27 (15 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein s14 (16 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el33 (12 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l8 (28 kDa, Protein from Solanum lycopersicum)
- S10_plectin domain-containing protein (19 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l38 (8 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el32 (15 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el39 (6 kDa, Protein from Solanum lycopersicum)
- S5 drbm domain-containing protein (30 kDa, Protein from Solanum lycopersicum)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s6 (28 kDa, Protein from Solanum lycopersicum)
- Trash domain-containing protein (18 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l18e/l15p domain-containing protein (20 kDa, Protein from Solanum lycopersicum)
- Ribosomal_s17_n domain-containing protein (17 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul5 (20 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l13 (23 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s8 (24 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el22 (13 kDa, Protein from Solanum lycopersicum)
- 80s ribosome (Complex from Solanum lycopersicum)
- 60s ribosomal protein l18a (21 kDa, Protein from Solanum lycopersicum)
- Spermine (202 Da, Ligand)
- 60s ribosomal protein el43 (10 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s24 (15 kDa, Protein from Solanum lycopersicum)
- 30s ribosomal protein s15, chloroplastic (17 kDa, Protein from Solanum lycopersicum)
- 5.8s rrna (53 kDa, RNA from Solanum lycopersicum)
- 40s ribosomal protein s30 (6 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul6 (22 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s7 (22 kDa, Protein from Solanum lycopersicum)
- Mrna (895 Da, RNA from Solanum lycopersicum)
- Kh type-2 domain-containing protein (26 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l18e/l15p domain-containing protein (16 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s3a (29 kDa, Protein from Solanum lycopersicum)
- 40s body ribosomal protein us12 (15 kDa, Protein from Solanum lycopersicum)
- Potassium ion (39 Da, Ligand)
- Ribosomal_s7 domain-containing protein (23 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l36 (12 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s4 (29 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein us9 (16 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l6e_n domain-containing protein (25 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein us19 (17 kDa, Protein from Solanum lycopersicum)
- Ribosomal_s10 domain-containing protein (13 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s27 (9 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l14e domain-containing protein (15 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el30 (12 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l37 (10 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein us13 (17 kDa, Protein from Solanum lycopersicum)
- Water (18 Da, Ligand)
- 40s ribosomal protein es28 (7 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l29 (6 kDa, Protein from Solanum lycopersicum)
- Pectinesterase (23 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l10 (24 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s25 (11 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein sa (32 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el21 (18 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l7ae domain-containing protein (29 kDa, Protein from Solanum lycopersicum)
- Beta-d-glucopyranose (180 Da, Ligand)
- Kow domain-containing protein (16 kDa, Protein from Solanum lycopersicum)
- Zinc ion (65 Da, Ligand)
- Similar to 60s ribosomal protein l35 (14 kDa, Protein from Solanum lycopersicum)
- Ubiquitin (14 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l23en domain-containing protein (17 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s26 (14 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l19 (24 kDa, Protein from Solanum lycopersicum)
- Mitogen-activated protein kinase (35 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul14 (15 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el42 (12 kDa, Protein from Solanum lycopersicum)
- Trna (589 Da, RNA from Solanum lycopersicum)
- 60s ribosomal protein l41 (3 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el31 (13 kDa, Protein from Solanum lycopersicum)
- 25s rrna (1 MDa, RNA from Solanum lycopersicum)
- 60s ribosomal protein el34 (13 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l28e domain-containing protein (16 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s21 (9 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein es19 (16 kDa, Protein from Solanum lycopersicum)
- Ribos_l4_asso_c domain-containing protein (44 kDa, Protein from Solanum lycopersicum)
- 50s ribosomal protein l22, chloroplastic (19 kDa, Protein from Solanum lycopersicum)
- 40s body ribosomal protein us4 (23 kDa, Protein from Solanum lycopersicum)
- Trna_1 (4 kDa, RNA from Solanum lycopersicum)
Human mitochondrial ribosome at 2.2 A resolution
Resolution: 2.21 Å
EM Method: Single-particle
Fitted PDBs: 7qi4
Q-score: 0.658
Singh V, Itoh Y, Del'Olio S, Hassan A, Naschberger A, Flygaard RK, Nobe Y, Izumikawa K, Aibara S, Andrell J, Whitford PC, Barrientos A, Taoka M, Amunts A
bioRxiv (2023) [ DOI: doi:10.1101/2023.05.24.542018 Pubmed: 37503168 ]
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Spermidine (145 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 39s ribosomal protein l17, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- 1,4-diaminobutane (88 Da, Ligand)
- 39s ribosomal protein l47, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l37, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l54, mitochondrial (15 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l52, mitochondrial (13 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l4, mitochondrial (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 39s ribosomal protein l35, mitochondrial (21 kDa, Protein from Homo sapiens)
- Mrna (10 kDa, RNA from Homo sapiens)
- 39s ribosomal protein s30, mitochondrial (50 kDa, Protein from Homo sapiens)
- Ribosomal protein 63, mitochondrial (12 kDa, Protein from Homo sapiens)
- E/e-trna (16 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l20, mitochondrial (17 kDa, Protein from Homo sapiens)
- P/p-trna (22 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l30, mitochondrial (18 kDa, Protein from Homo sapiens)
- A/a-trna (6 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l43, mitochondrial (23 kDa, Protein from Homo sapiens)
- Spermine (202 Da, Ligand)
- 39s ribosomal protein l49, mitochondrial (19 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l2, mitochondrial (33 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l39, mitochondrial (38 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l40, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l53, mitochondrial (12 kDa, Protein from Homo sapiens)
- Peptidyl-trna hydrolase ict1, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l13, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l18, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l41, mitochondrial (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 39s ribosomal protein s18a, mitochondrial (22 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l11, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l21, mitochondrial (22 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l23, mitochondrial (17 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l46, mitochondrial (31 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l12, mitochondrial (21 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l9, mitochondrial (30 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l42, mitochondrial (16 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l32, mitochondrial (21 kDa, Protein from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l44, mitochondrial (37 kDa, Protein from Homo sapiens)
- Valine (117 Da, Ligand)
- 16s mitochondrial rrna (499 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l48, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 39s ribosomal protein l36, mitochondrial (11 kDa, Protein from Homo sapiens)
- Human mitochondrial ribosome (Complex from Homo sapiens)
- 39s ribosomal protein l3, mitochondrial (38 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l27, mitochondrial (16 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 39s ribosomal protein l22, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l51, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l50, mitochondrial (18 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l1, mitochondrial (36 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l15, mitochondrial (33 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l33, mitochondrial (7 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l16, mitochondrial (28 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l19, mitochondrial (33 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l28, mitochondrial (30 kDa, Protein from Homo sapiens)
- Mitochondrial trnaval (22 kDa, RNA from Homo sapiens)
- Mrps21 isoform 1 (10 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l24, mitochondrial (24 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l38, mitochondrial (44 kDa, Protein from Homo sapiens)
- Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (13 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l55, mitochondrial (15 kDa, Protein from Homo sapiens)
- Growth arrest and dna damage-inducible proteins-interacting protein 1 (25 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l34, mitochondrial (10 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l45, mitochondrial (35 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l10, mitochondrial (29 kDa, Protein from Homo sapiens)
Specific features and methylation sites of a plant ribosome. 60S ribosomal subunit.
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 7qiw
Q-score: 0.686
Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lison P, Taoka M, Amunts A
Plant Commun. (2022) 3 pp. 100342-100342 [ Pubmed: 35643637 DOI: doi:10.1016/j.xplc.2022.100342 ]
- Ribosomal protein l15 (24 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l18a (21 kDa, Protein from Solanum lycopersicum)
- Kow domain-containing protein (16 kDa, Protein from Solanum lycopersicum)
- Zinc ion (65 Da, Ligand)
- Similar to 60s ribosomal protein l35 (14 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l36 (12 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l23en domain-containing protein (17 kDa, Protein from Solanum lycopersicum)
- 5s rrna (38 kDa, RNA from Solanum lycopersicum)
- Ribosomal protein l19 (24 kDa, Protein from Solanum lycopersicum)
- Putative 60s ribosomal protein l27a-3-like (16 kDa, Protein from Solanum lycopersicum)
- Thaliana 60s ribosomal protein l7 (28 kDa, Protein from Solanum lycopersicum)
- Spermidine (145 Da, Ligand)
- Ribosomal_l6e_n domain-containing protein (25 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l3 (44 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul14 (15 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el42 (12 kDa, Protein from Solanum lycopersicum)
- Spermine (202 Da, Ligand)
- 60s ribosomal protein el43 (10 kDa, Protein from Solanum lycopersicum)
- Trna (589 Da, RNA from Solanum lycopersicum)
- 60s ribosomal protein ul13 (23 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l27 (15 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el33 (12 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l8 (28 kDa, Protein from Solanum lycopersicum)
- 5.8s rrna (53 kDa, RNA from Solanum lycopersicum)
- 60s ribosomal protein l38 (8 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el31 (13 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el32 (15 kDa, Protein from Solanum lycopersicum)
- Ubiquitin-like domain-containing protein (14 kDa, Protein from Solanum lycopersicum)
- 25s rrna (1 MDa, RNA from Solanum lycopersicum)
- 60s ribosomal protein ul6 (22 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l14e domain-containing protein (15 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el34 (13 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l28e domain-containing protein (16 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el39 (6 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal subunit (Complex from Solanum lycopersicum)
- Magnesium ion (24 Da, Ligand)
- Ribosomal protein l37 (10 kDa, Protein from Solanum lycopersicum)
- Ribos_l4_asso_c domain-containing protein (44 kDa, Protein from Solanum lycopersicum)
- Water (18 Da, Ligand)
- 60s ribosomal protein l29 (6 kDa, Protein from Solanum lycopersicum)
- Trash domain-containing protein (18 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l7ae domain-containing protein (12 kDa, Protein from Solanum lycopersicum)
- 50s ribosomal protein l22, chloroplastic (19 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l10 (24 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l18e/l15p domain-containing protein (20 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul5 (20 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l13 (23 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el21 (18 kDa, Protein from Solanum lycopersicum)
- Potassium ion (39 Da, Ligand)
- Ribosomal_l7ae domain-containing protein (29 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el22 (13 kDa, Protein from Solanum lycopersicum)
Specific features and methylation sites of a plant ribosome. 40S body ribosomal subunit.
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 7qix
Q-score: 0.648
Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lison P, Taoka M, Amunts A
Plant Commun. (2022) 3 pp. 100342-100342 [ Pubmed: 35643637 DOI: doi:10.1016/j.xplc.2022.100342 ]
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s26 (14 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l19 (24 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s15a-1 (14 kDa, Protein from Solanum lycopersicum)
- 18s rrna body (583 kDa, RNA from Solanum lycopersicum)
- 40s ribosomal protein s17 (16 kDa, Protein from Solanum lycopersicum)
- 40s body ribosomal protein es4 (29 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s24 (15 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein s14 (16 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l41 (3 kDa, Protein from Solanum lycopersicum)
- 30s ribosomal protein s15, chloroplastic (17 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s30 (6 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s7 (22 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s27 (9 kDa, Protein from Solanum lycopersicum)
- S5 drbm domain-containing protein (30 kDa, Protein from Solanum lycopersicum)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s21 (9 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s6 (28 kDa, Protein from Solanum lycopersicum)
- Water (18 Da, Ligand)
- 40s ribosomal protein s3a (29 kDa, Protein from Solanum lycopersicum)
- 40s body ribosomal protein us12 (15 kDa, Protein from Solanum lycopersicum)
- 40s body ribosomal protein us4 (23 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein sa (32 kDa, Protein from Solanum lycopersicum)
- Ribosomal_s17_n domain-containing protein (17 kDa, Protein from Solanum lycopersicum)
- Potassium ion (39 Da, Ligand)
- 40s ribosomal protein s8 (24 kDa, Protein from Solanum lycopersicum)
- 40s body ribosomal subunit (Complex from Solanum lycopersicum)
Specific features and methylation sites of a plant ribosome
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 7qiy
Q-score: 0.646
Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lison P, Taoka M, Amunts A
Plant Commun. (2022) 3 pp. 100342-100342 [ Pubmed: 35643637 DOI: doi:10.1016/j.xplc.2022.100342 ]
- 40s head ribosomal subunit (Complex from Solanum lycopersicum)
- Beta-d-glucopyranose (180 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Mitogen-activated protein kinase (35 kDa, Protein from Solanum lycopersicum)
- 1,4-diaminobutane (88 Da, Ligand)
- 40s head ribosomal protein us9 (16 kDa, Protein from Solanum lycopersicum)
- 18s rrna head (582 kDa, RNA from Solanum lycopersicum)
- 40s ribosomal protein s29 (6 kDa, Protein from Solanum lycopersicum)
- S10_plectin domain-containing protein (19 kDa, Protein from Solanum lycopersicum)
- Ribosomal_s10 domain-containing protein (13 kDa, Protein from Solanum lycopersicum)
- 40s head ribosomal protein es28 (7 kDa, Protein from Solanum lycopersicum)
- Trna (4 kDa, RNA from Solanum lycopersicum)
- Mrna (895 Da, RNA from Solanum lycopersicum)
- Magnesium ion (24 Da, Ligand)
- 40s head ribosomal protein us19 (17 kDa, Protein from Solanum lycopersicum)
- 40s head ribosomal protein us13 (17 kDa, Protein from Solanum lycopersicum)
- Water (18 Da, Ligand)
- Kh type-2 domain-containing protein (26 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s17 (16 kDa, Protein from Solanum lycopersicum)
- 40s head ribosomal protein es19 (16 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s25 (11 kDa, Protein from Solanum lycopersicum)
- Potassium ion (39 Da, Ligand)
- Ribosomal_s7 domain-containing protein (23 kDa, Protein from Solanum lycopersicum)
Specific features and methylation sites of a plant ribosome. 80S translating ribosome (A/A-P/P-E/E).
Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lison P, Taoka M, Amunts A
Plant Commun. (2022) 3 pp. 100342-100342 [ Pubmed: 35643637 DOI: doi:10.1016/j.xplc.2022.100342 ]
Specific features and methylation sites of a plant ribosome. 80S translating ribosome (A/P-P/E).
Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lison P, Taoka M, Amunts A
Plant Commun. (2022) 3 pp. 100342-100342 [ Pubmed: 35643637 DOI: doi:10.1016/j.xplc.2022.100342 ]
Specific features and methylation sites of a plant ribosome. 80S ribosome consensus map.
Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lison P, Taoka M, Amunts A
Plant Commun. (2022) 3 pp. 100342-100342 [ Pubmed: 35643637 DOI: doi:10.1016/j.xplc.2022.100342 ]