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 RIO1(kd)-StHA late pre-40S particle, structural state B (post 18S rRNA cleavage)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6zv6
Q-score: 0.468
Plassart L, Shayan R, Montellese C, Rinaldi D, Larburu N, Pichereaux C, Froment C, Lebaron S, O'Donohue MF, Kutay U, Marcoux J, Gleizes PE, Plisson-Chastang C
eLife (2021) 10 [ Pubmed: 33908345 DOI: doi:10.7554/eLife.61254 ]
- 40s ribosomal protein s15 (17 kDa, Protein from Human)
- Serine/threonine-protein kinase rio1 (65 kDa, Protein from Human)
- 40s ribosomal protein s21 (9 kDa, Protein from Human)
- 40s ribosomal protein s26 (13 kDa, Protein from Human)
- 40s ribosomal protein s30 (6 kDa, Protein from Human)
- 40s ribosomal protein s8 (24 kDa, Protein from Human)
- 40s ribosomal protein s16 (16 kDa, Protein from Human)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Human)
- 40s ribosomal protein s12 (14 kDa, Protein from Human)
- 40s ribosomal protein sa (32 kDa, Protein from Human)
- 40s ribosomal protein s28 (7 kDa, Protein from Human)
- 40s ribosomal protein s10 (18 kDa, Protein from Human)
- 40s ribosomal protein s17 (15 kDa, Protein from Human)
- 40s ribosomal protein s25 (13 kDa, Protein from Human)
- 40s ribosomal protein s27 (9 kDa, Protein from Human)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 40s ribosomal protein s23 (15 kDa, Protein from Human)
- 40s ribosomal protein s19 (16 kDa, Protein from Human)
- 40s ribosomal protein s29 (6 kDa, Protein from Human)
- 40s ribosomal protein s11 (18 kDa, Protein from Human)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Human)
- 40s ribosomal protein s3a (30 kDa, Protein from Human)
- 40s ribosomal protein s7 (22 kDa, Protein from Human)
- Water (18 Da, Ligand)
- 40s ribosomal protein s6 (28 kDa, Protein from Human)
- 40s ribosomal protein s2 (31 kDa, Protein from Human)
- 40s ribosomal protein s9 (22 kDa, Protein from Human)
- 40s ribosomal protein s18 (17 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- 18s ribosomal rna (602 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Human)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s14 (16 kDa, Protein from Human)
- 40s ribosomal protein s5 (22 kDa, Protein from Human)
- 40s ribosomal protein s15a (14 kDa, Protein from Human)
- Human cytoplasmic late precursor to the small ribosomal subunit, purified using rio1(kd)-stha as bait. structural state b (post 18s rrna maturation) (1 MDa, Complex from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Human)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Human)
- 40s ribosomal protein s20 (13 kDa, Protein from Human)
- 40s ribosomal protein s3 (26 kDa, Protein from Human)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6zvh
Q-score: 0.557
Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M, Paulo JA, Harper W, Bennett EJ, Beckmann R, Green R
eLife (2020) 9 [ Pubmed: 32744497 DOI: doi:10.7554/eLife.58828 ]
- 40s ribosomal protein s7 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (27 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (4 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 18s rrna (561 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s12 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (25 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (7 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Cell growth-regulating nucleolar protein (8 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Endothelial differentiation-related factor 1 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (17 kDa, Protein from Homo sapiens)
- Edf1-ribosome complex (Complex from Homo sapiens)
- 40s ribosomal protein s25 (8 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (34 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- E-site trna (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
2.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 5nwy
Q-score: 0.558
Su T, Cheng J, Sohmen D, Hedman R, Berninghausen O, von Heijne G, Wilson DN, Beckmann R
eLife (2017) 6 [ DOI: doi:10.7554/eLife.25642 Pubmed: 28556777 ]
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s7 (17 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s2 (25 kDa, Protein from Escherichia coli (strain K12))
- Vemp-stalled ribosome-nascent chain complex (Complex from Escherichia coli K-12)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli (strain K12))
- 16s rrna (498 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli (strain K12))
- Vemp nascent chain (20 kDa, Protein from Vibrio alginolyticus)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli (strain K12))
- Vemp-stalled ribosome-nascent chain complex (Complex)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
- 23s rrna (941 kDa, RNA from Escherichia coli K-12)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli (strain K12))
- Mrna (1 kDa, RNA from Vibrio alginolyticus)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli (strain K12))
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
- Vemp-stalled ribosome-nascent chain complex (Complex from Vibrio alginolyticus)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain K12))
- Gln-trna (24 kDa, RNA from Escherichia coli)