Cryo-EM structure of the TnpB-omegaRNA-target DNA ternary complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8h1j
Q-score: 0.453
Nakagawa R, Hirano H, Omura SN, Nety S, Kannan S, Altae-Tran H, Yao X, Sakaguchi Y, Ohira T, Wu WY, Nakayama H, Shuto Y, Tanaka T, Sano FK, Kusakizako T, Kise Y, Itoh Y, Dohmae N, van der Oost J, Suzuki T, Zhang F, Nureki O
Nature (2023) 616 pp. 390-397 [ DOI: doi:10.1038/s41586-023-05933-9 Pubmed: 37020030 ]
- Rna-guided dna endonuclease tnpb (46 kDa, Protein from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Zinc ion (65 Da, Ligand)
- Non-target strand (10 kDa, DNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Tnpb-omegarna-target dna ternary complex (Complex from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Omegarna (130-mer) (79 kDa, RNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Target strand (10 kDa, DNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7x8y
Q-score: 0.318
Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Moriyama S, Takahashi Y, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Itoh Y, Imai M, Maemura T, Furusawa Y, Ueki H, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T
iScience (2022) 25 pp. 105596-105596 [ DOI: doi:10.1016/j.isci.2022.105596 Pubmed: 36406861 ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab159 (560 kDa, Complex from Homo sapiens)
- Ab159 light chain (26 kDa, Protein from Homo sapiens)
- Ab159 heavy chain (28 kDa, Protein from Homo sapiens)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7x8z
Q-score: 0.368
Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Moriyama S, Takahashi Y, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Itoh Y, Imai M, Maemura T, Furusawa Y, Ueki H, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T
iScience (2022) 25 pp. 105596-105596 [ DOI: doi:10.1016/j.isci.2022.105596 Pubmed: 36406861 ]
- The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab354 (560 kDa, Complex from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ab188 light chain (27 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ab188 heavy chain (28 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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 [ DOI: doi:10.1016/j.xplc.2022.100342 Pubmed: 35643637 ]
- 40s ribosomal protein es19 (16 kDa, Protein from Solanum lycopersicum)
- Ribosomal_s7 domain-containing protein (23 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s4 (29 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s30 (6 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el21 (18 kDa, Protein from Solanum lycopersicum)
- Potassium ion (39 Da, Ligand)
- 60s ribosomal protein l13 (23 kDa, Protein from Solanum lycopersicum)
- 50s ribosomal protein l22, chloroplastic (19 kDa, Protein from Solanum lycopersicum)
- Water (18 Da, Ligand)
- Ribosomal protein s14 (16 kDa, Protein from Solanum lycopersicum)
- Ribosomal_s10 domain-containing protein (13 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l41 (3 kDa, Protein from Solanum lycopersicum)
- Mitogen-activated protein kinase (35 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul5 (20 kDa, Protein from Solanum lycopersicum)
- Ubiquitin (14 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el42 (12 kDa, Protein from Solanum lycopersicum)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l29 (6 kDa, Protein from Solanum lycopersicum)
- S5 drbm domain-containing protein (30 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l23en domain-containing protein (17 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s3a (29 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s25 (11 kDa, Protein from Solanum lycopersicum)
- Trash domain-containing protein (18 kDa, Protein from Solanum lycopersicum)
- Kow domain-containing protein (16 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l15 (24 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el33 (12 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein us9 (16 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein us14 (6 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l6e_n domain-containing protein (25 kDa, Protein from Solanum lycopersicum)
- Spermine (202 Da, Ligand)
- 40s ribosomal protein s15a-1 (14 kDa, Protein from Solanum lycopersicum)
- Ribosomal_s17_n domain-containing protein (17 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l36 (12 kDa, Protein from Solanum lycopersicum)
- Spermidine (145 Da, Ligand)
- 40s ribosomal protein sa (32 kDa, Protein from Solanum lycopersicum)
- 80s ribosome (Complex from Solanum lycopersicum)
- 40s ribosomal protein s26 (14 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein us19 (17 kDa, Protein from Solanum lycopersicum)
- Beta-d-glucopyranose (180 Da, Ligand)
- 60s ribosomal protein el43 (10 kDa, Protein from Solanum lycopersicum)
- Similar to 60s ribosomal protein l35 (14 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l18e/l15p domain-containing protein (16 kDa, Protein from Solanum lycopersicum)
- Ribos_l4_asso_c domain-containing protein (44 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l10 (24 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s21 (9 kDa, Protein from Solanum lycopersicum)
- Pectinesterase (23 kDa, Protein from Solanum lycopersicum)
- 25s rrna (1 MDa, RNA from Solanum lycopersicum)
- 40s ribosomal protein s8 (24 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el22 (13 kDa, Protein from Solanum lycopersicum)
- Kh type-2 domain-containing protein (26 kDa, Protein from Solanum lycopersicum)
- 18s (583 kDa, RNA from Solanum lycopersicum)
- 60s ribosomal protein el34 (13 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el30 (12 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s7 (22 kDa, Protein from Solanum lycopersicum)
- 5s rrna (38 kDa, RNA from Solanum lycopersicum)
- 60s ribosomal protein ul6 (22 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l19 (24 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l18e/l15p domain-containing protein (20 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s17 (16 kDa, Protein from Solanum lycopersicum)
- 40s body ribosomal protein us4 (23 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s6 (28 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l7ae domain-containing protein (29 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l27 (15 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l3 (44 kDa, Protein from Solanum lycopersicum)
- Magnesium ion (24 Da, Ligand)
- Ribosomal protein l37 (10 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s27 (9 kDa, Protein from Solanum lycopersicum)
- 40s body ribosomal protein us12 (15 kDa, Protein from Solanum lycopersicum)
- Trna_1 (4 kDa, RNA from Solanum lycopersicum)
- 30s ribosomal protein s15, chloroplastic (17 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l18a (21 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul14 (15 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein s24 (15 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l28e domain-containing protein (16 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l8 (28 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el32 (15 kDa, Protein from Solanum lycopersicum)
- Trna (589 Da, RNA from Solanum lycopersicum)
- 60s ribosomal protein l38 (8 kDa, Protein from Solanum lycopersicum)
- 1,4-diaminobutane (88 Da, Ligand)
- 60s ribosomal protein el39 (6 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein us13 (17 kDa, Protein from Solanum lycopersicum)
- 5.8s rrna (53 kDa, RNA from Solanum lycopersicum)
- Ribosomal_l14e domain-containing protein (15 kDa, Protein from Solanum lycopersicum)
- S10_plectin domain-containing protein (19 kDa, Protein from Solanum lycopersicum)
- Thaliana 60s ribosomal protein l7 (28 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el31 (13 kDa, Protein from Solanum lycopersicum)
- 40s ribosomal protein es28 (7 kDa, Protein from Solanum lycopersicum)
- Mrna (895 Da, RNA from Solanum lycopersicum)
Human mitochondrial ribosome small subunit in complex with IF3, GMPPMP and streptomycin
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 7p2e
Q-score: 0.667
Itoh Y, Singh V, Khawaja A, Naschberger A, Nguyen MD, Rorbach J, Amunts A
eLife (2022) 11 [ DOI: doi:10.7554/eLife.77460 Pubmed: 36480258 ]
- Translation initiation factor if-3, mitochondrial (Complex from Homo sapiens)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Small subunit of human mitochondrial ribosome in complex (Complex from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- Small subunit of human mitochondrial ribosome in complex with initiation factor 3 (Complex)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Spermine (202 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- Translation initiation factor if-3, mitochondrial (32 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (13 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
- [(2~{s},3~{s},4~{s},5~{r},6~{s})-2-[(2~{r},3~{r},4~{r},5~{s})-2-[(1~{r},2~{s},3~{r},4~{r},5~{s},6~{r})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium (602 Da, Ligand)
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
Nat Commun (2024) 15 pp. 4272-4272 [ Pubmed: 38769321 DOI: doi:10.1038/s41467-024-48163-x ]
- 39s ribosomal protein l21, mitochondrial (22 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 39s ribosomal protein l34, mitochondrial (10 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l55, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l10, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l54, mitochondrial (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 39s ribosomal protein l13, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l32, mitochondrial (21 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 39s ribosomal protein l37, mitochondrial (48 kDa, Protein from Homo sapiens)
- Human mitochondrial ribosome (Complex from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l24, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l51, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l11, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l46, mitochondrial (31 kDa, Protein from Homo sapiens)
- A/a-trna (6 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l19, mitochondrial (33 kDa, Protein from Homo sapiens)
- Peptidyl-trna hydrolase ict1, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l2, mitochondrial (33 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l20, mitochondrial (17 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l48, mitochondrial (23 kDa, Protein from Homo sapiens)
- Spermine (202 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l49, mitochondrial (19 kDa, Protein from Homo sapiens)
- 39s ribosomal protein s18a, mitochondrial (22 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Spermidine (145 Da, Ligand)
- 39s ribosomal protein l50, mitochondrial (18 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)
- 39s ribosomal protein l30, mitochondrial (18 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l3, mitochondrial (38 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l47, mitochondrial (29 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- Valine (117 Da, Ligand)
- 39s ribosomal protein l4, mitochondrial (34 kDa, Protein from Homo sapiens)
- Growth arrest and dna damage-inducible proteins-interacting protein 1 (25 kDa, Protein from Homo sapiens)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 39s ribosomal protein l44, mitochondrial (37 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l40, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l9, mitochondrial (30 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l16, mitochondrial (28 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l28, mitochondrial (30 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l12, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l35, mitochondrial (21 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l38, mitochondrial (44 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Mrps21 isoform 1 (10 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l22, mitochondrial (23 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l52, mitochondrial (13 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l27, mitochondrial (16 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 39s ribosomal protein l39, mitochondrial (38 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l17, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l36, mitochondrial (11 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l42, mitochondrial (16 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l45, mitochondrial (35 kDa, Protein from Homo sapiens)
- Ribosomal protein 63, mitochondrial (12 kDa, Protein from Homo sapiens)
- E/e-trna (16 kDa, RNA from Homo sapiens)
- Mitochondrial trnaval (22 kDa, RNA from Homo sapiens)
- 1,4-diaminobutane (88 Da, Ligand)
- 39s ribosomal protein l41, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 16s mitochondrial rrna (499 kDa, RNA 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)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 39s ribosomal protein s30, mitochondrial (50 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l23, mitochondrial (17 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- Mrna (10 kDa, RNA from Homo sapiens)
- Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (13 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l53, mitochondrial (12 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l1, mitochondrial (36 kDa, Protein from Homo sapiens)
- 39s ribosomal protein l43, mitochondrial (23 kDa, Protein from Homo sapiens)
- P/p-trna (22 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s15, 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 [ DOI: doi:10.1016/j.xplc.2022.100342 Pubmed: 35643637 ]
- Trash domain-containing protein (18 kDa, Protein from Solanum lycopersicum)
- Kow domain-containing protein (16 kDa, Protein from Solanum lycopersicum)
- 25s rrna (1 MDa, RNA from Solanum lycopersicum)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el22 (13 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l15 (24 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l18a (21 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul14 (15 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el21 (18 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 l8 (28 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el32 (15 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el33 (12 kDa, Protein from Solanum lycopersicum)
- 5s rrna (38 kDa, RNA from Solanum lycopersicum)
- Trna (589 Da, RNA from Solanum lycopersicum)
- 60s ribosomal subunit (Complex from Solanum lycopersicum)
- 60s ribosomal protein l38 (8 kDa, Protein from Solanum lycopersicum)
- Potassium ion (39 Da, Ligand)
- Ribosomal_l6e_n domain-containing protein (25 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul6 (22 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l19 (24 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el39 (6 kDa, Protein from Solanum lycopersicum)
- Spermine (202 Da, Ligand)
- 60s ribosomal protein l13 (23 kDa, Protein from Solanum lycopersicum)
- 5.8s rrna (53 kDa, RNA from Solanum lycopersicum)
- 50s ribosomal protein l22, chloroplastic (19 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l18e/l15p domain-containing protein (20 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l36 (12 kDa, Protein from Solanum lycopersicum)
- Water (18 Da, Ligand)
- Ribosomal_l14e domain-containing protein (15 kDa, Protein from Solanum lycopersicum)
- Spermidine (145 Da, Ligand)
- Thaliana 60s ribosomal protein l7 (28 kDa, Protein from Solanum lycopersicum)
- Putative 60s ribosomal protein l27a-3-like (16 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l7ae domain-containing protein (29 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l27 (15 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l3 (44 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul5 (20 kDa, Protein from Solanum lycopersicum)
- Ubiquitin-like domain-containing protein (14 kDa, Protein from Solanum lycopersicum)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein el42 (12 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l7ae domain-containing protein (12 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein ul13 (23 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el31 (13 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein el43 (10 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 l29 (6 kDa, Protein from Solanum lycopersicum)
- Ribos_l4_asso_c domain-containing protein (44 kDa, Protein from Solanum lycopersicum)
- Ribosomal protein l37 (10 kDa, Protein from Solanum lycopersicum)
- 60s ribosomal protein l10 (24 kDa, Protein from Solanum lycopersicum)
- Ribosomal_l23en domain-containing protein (17 kDa, Protein from Solanum lycopersicum)
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 7pnt
Q-score: 0.516
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Mus musculus)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (77 kDa, Protein from Mus musculus)
- 28s ribosomal protein s31, mitochondrial (43 kDa, Protein from Mus musculus)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Mus musculus)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18b, mitochondrial (28 kDa, Protein from Mus musculus)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Mus musculus)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Mus musculus)
- 12s mitochondrial rrna (306 kDa, RNA from Mus musculus)
- 28s ribosomal protein s14, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Mus musculus)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Mus musculus)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Mus musculus)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Mus musculus)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Mus musculus)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18c, mitochondrial (16 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s2, mitochondrial (32 kDa, Protein from Mus musculus)
- Dimethyladenosine transferase 1, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s29, mitochondrial (44 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Putative ribosome-binding factor a, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s25, mitochondrial (19 kDa, Protein from Mus musculus)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (13 kDa, Protein from Mus musculus)
- 28s ribosomal protein s10, mitochondrial (18 kDa, Protein from Mus musculus)
- Aurora kinase a-interacting protein (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Mus musculus)
- 28s ribosomal protein s23, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s26, mitochondrial (23 kDa, Protein from Mus musculus)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 7pnu
Q-score: 0.552
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Mus musculus)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (77 kDa, Protein from Mus musculus)
- 28s ribosomal protein s31, mitochondrial (43 kDa, Protein from Mus musculus)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Mus musculus)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18b, mitochondrial (28 kDa, Protein from Mus musculus)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Mus musculus)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Mus musculus)
- 12s mitochondrial rrna (306 kDa, RNA from Mus musculus)
- 28s ribosomal protein s14, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Mus musculus)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Mus musculus)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Mus musculus)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Mus musculus)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Mus musculus)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18c, mitochondrial (16 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s2, mitochondrial (32 kDa, Protein from Mus musculus)
- 28s ribosomal protein s29, mitochondrial (44 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Putative ribosome-binding factor a, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s25, mitochondrial (19 kDa, Protein from Mus musculus)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (13 kDa, Protein from Mus musculus)
- 28s ribosomal protein s10, mitochondrial (18 kDa, Protein from Mus musculus)
- Aurora kinase a-interacting protein (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Mus musculus)
- 28s ribosomal protein s23, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s26, mitochondrial (23 kDa, Protein from Mus musculus)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 7pnv
Q-score: 0.544
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Mus musculus)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (77 kDa, Protein from Mus musculus)
- 28s ribosomal protein s31, mitochondrial (43 kDa, Protein from Mus musculus)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Mus musculus)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 12s mitochondrial rrna (306 kDa, RNA from Mus musculus)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18b, mitochondrial (28 kDa, Protein from Mus musculus)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Mus musculus)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s14, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Mus musculus)
- 12s rrna n4-methylcytidine methyltransferase (45 kDa, Protein from Mus musculus)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Mus musculus)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Mus musculus)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Mus musculus)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Mus musculus)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18c, mitochondrial (16 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s2, mitochondrial (32 kDa, Protein from Mus musculus)
- 28s ribosomal protein s29, mitochondrial (44 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Putative ribosome-binding factor a, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s25, mitochondrial (19 kDa, Protein from Mus musculus)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (13 kDa, Protein from Mus musculus)
- 28s ribosomal protein s10, mitochondrial (18 kDa, Protein from Mus musculus)
- Aurora kinase a-interacting protein (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Mus musculus)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Mus musculus)
- 28s ribosomal protein s23, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s26, mitochondrial (23 kDa, Protein from Mus musculus)