Cryo-EM structure of the plant 80S ribosome
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8b2l
Q-score: 0.639
Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R
Nat Plants (2023) 9 pp. 987-1000 [ Pubmed: 37156858 DOI: doi:10.1038/s41477-023-01407-y ]
- 40s ribosomal protein s24 (15 kDa, Protein from Nicotiana tabacum)
- Ul15 (60s ribosomal protein l27a) (16 kDa, Protein from Nicotiana tabacum)
- 5.8s rrna (52 kDa, RNA from Nicotiana tabacum)
- 60s ribosomal protein l32-1 (15 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l18-2-like (20 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s19-3 (16 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l24-like (18 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s16 (16 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l38 (8 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l23a (17 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l21-1-like (18 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l22-2-like (14 kDa, Protein from Nicotiana tabacum)
- El27 (60s ribosomal protein l27) (15 kDa, Protein from Nicotiana tabacum)
- Potassium ion (39 Da, Ligand)
- 25s rrna (1 MDa, RNA from Nicotiana tabacum)
- 40s ribosomal protein s18 (17 kDa, Protein from Nicotiana tabacum)
- Ribosomal protein l19 (25 kDa, Protein from Nicotiana tabacum)
- Ubiquitin-40s ribosomal protein s27a-like (17 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s11-like (17 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l7a (29 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s8 (25 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l14-1 (15 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s10-1-like (23 kDa, Protein from Nicotiana tabacum)
- Ul4 (60s ribosomal protein l4) (44 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s15-like (17 kDa, Protein from Nicotiana tabacum)
- Spermidine (145 Da, Ligand)
- Guanine nucleotide-binding protein subunit beta-like protein (36 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s12 (15 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l7-4-like (28 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l18a (21 kDa, Protein from Nicotiana tabacum)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l44 (12 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein sa (35 kDa, Protein from Nicotiana tabacum)
- Trna (24 kDa, RNA from Nicotiana tabacum)
- 60s ribosomal protein l34 (13 kDa, Protein from Nicotiana tabacum)
- Spermine (202 Da, Ligand)
- Ul3 (60s ribosomal protein l3) (44 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s28 (7 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l35-like (14 kDa, Protein from Nicotiana tabacum)
- Ul5 (60s ribosomal protein l11) (20 kDa, Protein from Nicotiana tabacum)
- 30s ribosomal protein s15, chloroplastic (17 kDa, Protein from Nicotiana tabacum)
- 5s rrna (38 kDa, RNA from Nicotiana tabacum)
- El6 (60s ribosomal protein l6) (25 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l13 (23 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s15a-1 (14 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s17-like (16 kDa, Protein from Nicotiana tabacum)
- El28 (60s ribosomal protein l28) (15 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s27 (9 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l29 (7 kDa, Protein from Nicotiana tabacum)
- El31 (60s ribosomal protein l31) (13 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s26 (14 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s20-2 (13 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s2-3-like (30 kDa, Protein from Nicotiana tabacum)
- 50s ribosomal protein l22, chloroplastic (20 kDa, Protein from Nicotiana tabacum)
- Mrna (3 kDa, RNA from Nicotiana tabacum)
- 60s ribosomal protein l37a (10 kDa, Protein from Nicotiana tabacum)
- Nascent chain (2 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s3-2-like (27 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l23 (15 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s14-2 (16 kDa, Protein from Nicotiana tabacum)
- Ribosomal protein l37 (10 kDa, Protein from Nicotiana tabacum)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Nicotiana tabacum)
- Ul13 (60s ribosomal protein l13a) (23 kDa, Protein from Nicotiana tabacum)
- Ul2 (60s ribosomal protein l8) (28 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l41 (3 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s4 (29 kDa, Protein from Nicotiana tabacum)
- El36 (60s ribosomal protein l36) (12 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s5-like (23 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l39-3 (6 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s9-2-like (23 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s30 (6 kDa, Protein from Nicotiana tabacum)
- Ul24 (60s ribosomal protein l26) (16 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s21 (9 kDa, Protein from Nicotiana tabacum)
- Ul16 (60s ribosomal protein l10) (25 kDa, Protein from Nicotiana tabacum)
- El33 (60s ribosomal protein l35a) (12 kDa, Protein from Nicotiana tabacum)
- 18s rrna (583 kDa, RNA from Nicotiana tabacum)
- 40s subunit of the cytosolic 80s ribosome from tobacco (Complex from Nicotiana tabacum)
- Water (18 Da, Ligand)
- 40s ribosomal protein s25 (11 kDa, Protein from Nicotiana tabacum)
- Ribosomal protein l15 (24 kDa, Protein from Nicotiana tabacum)
- Ul6 (60s ribosomal protein l9) (22 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s23 (15 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s7 (22 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s29 (6 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l30-like (12 kDa, Protein from Nicotiana tabacum)
- 60s ribosomal protein l5-like (34 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s6 (28 kDa, Protein from Nicotiana tabacum)
- 40s ribosomal protein s3a (29 kDa, Protein from Nicotiana tabacum)
Cryo-EM structure of the plant 40S subunit
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 8auv
Q-score: 0.622
Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R
Nat Plants (2023) 9 pp. 987-1000 [ Pubmed: 37156858 DOI: doi:10.1038/s41477-023-01407-y ]
- Spermidine (145 Da, Ligand)
- Us2 (40s ribosomal protein sa) (35 kDa, Protein from Nicotiana tabacum)
- Es10 (40s ribosomal protein s10) (23 kDa, Protein from Nicotiana tabacum)
- Es19 (40s ribosomal protein s19) (16 kDa, Protein from Nicotiana tabacum)
- Us19 (40s ribosomal protein s15) (17 kDa, Protein from Nicotiana tabacum)
- Us13 (40s ribosomal protein s18) (17 kDa, Protein from Nicotiana tabacum)
- Us4 (40s ribosomal protein s9) (23 kDa, Protein from Nicotiana tabacum)
- Es30 (40s ribosomal protein s30) (6 kDa, Protein from Nicotiana tabacum)
- Us14 (40s ribosomal protein s29) (6 kDa, Protein from Nicotiana tabacum)
- Es12 (40s ribosomal protein s12) (15 kDa, Protein from Nicotiana tabacum)
- Es27 (40s ribosomal protein s27) (9 kDa, Protein from Nicotiana tabacum)
- Es25 (40s ribosomal protein s25) (11 kDa, Protein from Nicotiana tabacum)
- Es6 (40s ribosomal protein s6) (28 kDa, Protein from Nicotiana tabacum)
- Us5 (40s ribosomal protein s2) (30 kDa, Protein from Nicotiana tabacum)
- Es26 (40s ribosomal protein s26) (14 kDa, Protein from Nicotiana tabacum)
- Es8 (40s ribosomal protein s8) (25 kDa, Protein from Nicotiana tabacum)
- Zinc ion (65 Da, Ligand)
- Spermine (202 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- Us9 (40s ribosomal protein s16) (16 kDa, Protein from Nicotiana tabacum)
- Us8 (40s ribosomal protein s15a) (14 kDa, Protein from Nicotiana tabacum)
- 18s rrna (583 kDa, RNA from Nicotiana tabacum)
- Mrna (3 kDa, RNA from Nicotiana tabacum)
- 40s subunit of the cytosolic 80s ribosome from tobacco (Complex from Nicotiana tabacum)
- Water (18 Da, Ligand)
- Es21 (40s ribosomal protein s21) (9 kDa, Protein from Nicotiana tabacum)
- Us15 (40s ribosomal protein s13) (17 kDa, Protein from Nicotiana tabacum)
- Us17 (40s ribosomal protein s11) (17 kDa, Protein from Nicotiana tabacum)
- Rack1 (guanine nucleotide-binding protein subunit beta-like protein) (36 kDa, Protein from Nicotiana tabacum)
- Es4 (40s ribosomal protein s4) (29 kDa, Protein from Nicotiana tabacum)
- Es28 (40s ribosomal protein s28) (7 kDa, Protein from Nicotiana tabacum)
- Es17 (40s ribosomal protein s17) (16 kDa, Protein from Nicotiana tabacum)
- Es31 (ubiquitin-40s ribosomal protein s27a) (17 kDa, Protein from Nicotiana tabacum)
- Es7 (40s ribosomal protein s7) (22 kDa, Protein from Nicotiana tabacum)
- Us11 (40s ribosomal protein s14) (16 kDa, Protein from Nicotiana tabacum)
- Es24 (40s ribosomal protein s24) (15 kDa, Protein from Nicotiana tabacum)
- Es1 (40s ribosomal protein s3a) (29 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- Us7 (40s ribosomal protein s5) (23 kDa, Protein from Nicotiana tabacum)
- Us12 (40s ribosomal protein s23) (15 kDa, Protein from Nicotiana tabacum)
- Us10 (40s ribosomal protein s20) (13 kDa, Protein from Nicotiana tabacum)
- Us3 (40s ribosomal protein s3) (27 kDa, Protein from Nicotiana tabacum)
Cryo-EM structure of the plant 60S subunit
Resolution: 2.14 Å
EM Method: Single-particle
Fitted PDBs: 8azw
Q-score: 0.675
Smirnova J, Loerke J, Kleinau G, Schmidt A, Burger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R
Nat Plants (2023) 9 pp. 987-1000 [ Pubmed: 37156858 DOI: doi:10.1038/s41477-023-01407-y ]
- Spermidine (145 Da, Ligand)
- El28 (60s ribosomal protein l28) (15 kDa, Protein from Nicotiana tabacum)
- El32 (60s ribosomal protein l32) (15 kDa, Protein from Nicotiana tabacum)
- El42 (60s ribosomal protein l42) (12 kDa, Protein from Nicotiana tabacum)
- Ul15 (60s ribosomal protein l27a) (16 kDa, Protein from Nicotiana tabacum)
- 5.8s rrna (52 kDa, RNA from Nicotiana tabacum)
- Ul14 (60s ribosomal protein l23) (15 kDa, Protein from Nicotiana tabacum)
- El31 (60s ribosomal protein l31) (13 kDa, Protein from Nicotiana tabacum)
- Ul24 (60s ribosomal protein l26) (16 kDa, Protein from Nicotiana tabacum)
- Zinc ion (65 Da, Ligand)
- El20 (60s ribosomal protein l18a) (21 kDa, Protein from Nicotiana tabacum)
- El24 (60s ribosomal protein l24) (18 kDa, Protein from Nicotiana tabacum)
- El41 (60s ribosomal protein l41) (3 kDa, Protein from Nicotiana tabacum)
- El27 (60s ribosomal protein l27) (15 kDa, Protein from Nicotiana tabacum)
- El29 (60s ribosomal protein l29) (7 kDa, Protein from Nicotiana tabacum)
- Spermine (202 Da, Ligand)
- El22 (60s ribosomal protein l22) (14 kDa, Protein from Nicotiana tabacum)
- Ul3 (60s ribosomal protein l3) (44 kDa, Protein from Nicotiana tabacum)
- Ul16 (60s ribosomal protein l10) (25 kDa, Protein from Nicotiana tabacum)
- Potassium ion (39 Da, Ligand)
- El33 (60s ribosomal protein l35a) (12 kDa, Protein from Nicotiana tabacum)
- El13 (60s ribosomal protein l13) (23 kDa, Protein from Nicotiana tabacum)
- El21 (60s ribosomal protein l21) (18 kDa, Protein from Nicotiana tabacum)
- 25s rrna (1 MDa, RNA from Nicotiana tabacum)
- 40s subunit of the cytosolic 80s ribosome from tobacco (Complex from Nicotiana tabacum)
- Ul5 (60s ribosomal protein l11) (20 kDa, Protein from Nicotiana tabacum)
- Water (18 Da, Ligand)
- Ul29 (60s ribosomal protein l35) (14 kDa, Protein from Nicotiana tabacum)
- El39 (60s ribosomal protein l39) (6 kDa, Protein from Nicotiana tabacum)
- El19 (60s ribosomal protein l19) (25 kDa, Protein from Nicotiana tabacum)
- Ul18 (60s ribosomal protein l5) (34 kDa, Protein from Nicotiana tabacum)
- El30 (60s ribosomal protein l30) (12 kDa, Protein from Nicotiana tabacum)
- Ul23 (60s ribosomal protein l23a) (17 kDa, Protein from Nicotiana tabacum)
- Nascent chain (2 kDa, Protein from Nicotiana tabacum)
- Ul6 (60s ribosomal protein l9) (22 kDa, Protein from Nicotiana tabacum)
- El8 (60s ribosomal protein l7a) (29 kDa, Protein from Nicotiana tabacum)
- El34 (60s ribosomal protein l34) (13 kDa, Protein from Nicotiana tabacum)
- El38 (60s ribosomal protein l38) (8 kDa, Protein from Nicotiana tabacum)
- El37 (60s ribosomal protein l37) (10 kDa, Protein from Nicotiana tabacum)
- El43 (60s ribosomal protein l37a) (10 kDa, Protein from Nicotiana tabacum)
- Ul30 (60s ribosomal protein l7) (28 kDa, Protein from Nicotiana tabacum)
- Ul13 (60s ribosomal protein l13a) (23 kDa, Protein from Nicotiana tabacum)
- 5s rrna (38 kDa, RNA from Nicotiana tabacum)
- El40 (60s ribosomal protein l40) (14 kDa, Protein from Nicotiana tabacum)
- El18 (60s ribosomal protein l18) (20 kDa, Protein from Nicotiana tabacum)
- El15 (60s ribosomal protein l15) (24 kDa, Protein from Nicotiana tabacum)
- El6 (60s ribosomal protein l6) (25 kDa, Protein from Nicotiana tabacum)
- Ul2 (60s ribosomal protein l8) (28 kDa, Protein from Nicotiana tabacum)
- Ul4 (60s ribosomal protein l4) (44 kDa, Protein from Nicotiana tabacum)
- Magnesium ion (24 Da, Ligand)
- El36 (60s ribosomal protein l36) (12 kDa, Protein from Nicotiana tabacum)
- Ul22 (60s ribosomal protein l17) (20 kDa, Protein from Nicotiana tabacum)
- El14 (60s ribosomal protein l14) (15 kDa, Protein from Nicotiana tabacum)
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 7piu
Q-score: 0.6
Heyder NA, Kleinau G, Speck D, Schmidt A, Paisdzior S, Szczepek M, Bauer B, Koch A, Gallandi M, Kwiatkowski D, Burger J, Mielke T, Beck-Sickinger AG, Hildebrand PW, Spahn CMT, Hilger D, Schacherl M, Biebermann H, Hilal T, Kuhnen P, Kobilka BK, Scheerer P
Cell Res (2021) 31 pp. 1176-1189 [ DOI: doi:10.1038/s41422-021-00569-8 Pubmed: 34561620 ]
- Water (18 Da, Ligand)
- Melanocortin receptor 4 (38 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- Isoform gnas-2 of guanine nucleotide-binding protein g(s) subunit alpha isoforms short (44 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Setmelanotide (other names rm-493; bim-22493; irc-022493; imcivree) (1 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Ternary complex of setmelanotide-activated melanocortin 4 receptor with heterotrimeric gs, further stabilized by addition of nanobody 35 (144 MDa, Complex from Homo sapiens)
- Camelid antibody fragment - nanobody 35 (14 kDa, Protein from Lama glama)
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 7piv
Q-score: 0.539
Heyder NA, Kleinau G, Speck D, Schmidt A, Paisdzior S, Szczepek M, Bauer B, Koch A, Gallandi M, Kwiatkowski D, Burger J, Mielke T, Beck-Sickinger AG, Hildebrand PW, Spahn CMT, Hilger D, Schacherl M, Biebermann H, Hilal T, Kuhnen P, Kobilka BK, Scheerer P
Cell Res (2021) 31 pp. 1176-1189 [ DOI: doi:10.1038/s41422-021-00569-8 Pubmed: 34561620 ]
- Water (18 Da, Ligand)
- Melanocortin receptor 4 (38 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- Isoform gnas-2 of guanine nucleotide-binding protein g(s) subunit alpha isoforms short (44 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Ternary complex of the ndp-alpha-msh activated melanocortin 4 receptor (mc4r) gs protein complex stabilized by nanobody 35 (144 MDa, Complex from Homo sapiens)
- Ndp-alpha-msh (other names afamelanotide; scenesse) (1 kDa, Protein from synthetic construct)
- Camelid antibody vhh fragment - nanobody 35 (14 kDa, Protein from Lama glama)
Mammalian 80S HCV-IRES complex, Classical
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 5flx
Q-score: 0.261
Yamamoto H, Collier M, Loerke J, Ismer J, Schmidt A, Hilal T, Sprink T, Yamamoto K, Mielke T, Burger J, Shaikh TR, Dabrowski M, Hildebrand PW, Scheerer P, Spahn CMT
EMBO J (2015) 34 pp. 3042-3058 [ DOI: doi:10.15252/embj.201592469 Pubmed: 26604301 ]
- 80s ribosome (4 MDa, Complex from Oryctolagus cuniculus)
- Mammalian 80s-hcv-ires complex, classical (4 MDa, Sample)
- Hcv-ires (162 kDa, RNA from Hepatitis C virus)
Cryo electron microscopy of actively translating human polysomes (POST state).
Behrmann E, Loerke J, Budkevich TV, Yamamoto K, Schmidt A, Penczek PA, Vos MR, Burger J, Mielke T, Scheerer P, Spahn CMT
Cell (2015) 161 pp. 845-857 [ Pubmed: 25957688 DOI: doi:10.1016/j.cell.2015.03.052 ]
- Native ribosomal complex from polysomes - post state (4 MDa, Sample)
- 80s ribosomal complex (4 MDa, Complex from Homo sapiens)