Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8ipa
Q-score: 0.471
Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T
Nat Chem Biol (2024) 20 pp. 605-614 [ Pubmed: 38267667 DOI: doi:10.1038/s41589-023-01513-0 ]
- 40s ribosomal protein us11 (16 kDa, Protein from Triticum aestivum)
- Wheat 80s ribosome stalled on aug-stop boron dependently with cycloheximide (Complex from Triticum aestivum)
- 40s ribosomal protein es17 (16 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el6 (24 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us15 (17 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul5 (20 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul6 (21 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul22 (19 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein el8 (29 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el21 (18 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el40 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el34 (13 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us19 (17 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us8 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal rna (1 MDa, RNA from Triticum aestivum)
- 60s ribosomal protein el18 (21 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el41 (3 kDa, Protein from Oryza sativa)
- 60s ribosomal protein ul3 (44 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el31 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el38 (8 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul15 (16 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es4 (30 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es25 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es1 (30 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el29 (6 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul13 (23 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el33 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es10 (20 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul2 (28 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul29 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul23 (16 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us13 (17 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul4 (44 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us17 (17 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us10 (14 kDa, Protein from Triticum aestivum)
- 5.8s ribosomal rna (51 kDa, RNA from Triticum aestivum)
- 60s ribosomal protein el24 (18 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us4 (22 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es28 (9 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul30 (28 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul18 (34 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el30 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us5 (29 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el37 (10 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es26 (16 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es19 (17 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el20 (21 kDa, Protein from Triticum aestivum)
- Eukaryotic release factor 1 (49 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el14 (15 kDa, Protein from Triticum aestivum)
- Rack1 (36 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es7 (22 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el42 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us2 (33 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us9 (16 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el27 (15 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us14 (6 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el36 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es6 (28 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el43 (10 kDa, Protein from Triticum aestivum)
- 5s ribosomal rna (38 kDa, RNA from Triticum aestivum)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein us3 (25 kDa, Protein from Triticum aestivum)
- 18s ribosomal rna (583 kDa, RNA from Triticum aestivum)
- 60s ribosomal protein el39 (9 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us12 (15 kDa, Protein from Triticum aestivum)
- 4-{(2r)-2-[(1s,3s,5s)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione (281 Da, Ligand)
- 40s ribosomal protein es30 (6 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el28 (16 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul16 (24 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es8 (25 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el19 (24 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es21 (9 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es27 (9 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es24 (15 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el15 (24 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul14 (15 kDa, Protein from Triticum aestivum)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein ul24 (17 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el22 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el13 (24 kDa, Protein from Triticum aestivum)
- Trnai (24 kDa, RNA from Triticum aestivum)
- 60s ribosomal protein el32 (15 kDa, Protein from Triticum aestivum)
- Mrna (2 kDa, RNA from Triticum aestivum)
- 40s ribosomal protein us7 (22 kDa, Protein from Triticum aestivum)
Wheat 80S ribosome pausing on AUG-Stop with cycloheximide
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8ipb
Q-score: 0.466
Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T
Nat Chem Biol (2024) 20 pp. 605-614 [ Pubmed: 38267667 DOI: doi:10.1038/s41589-023-01513-0 ]
- 40s ribosomal protein us11 (16 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es17 (16 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el6 (24 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us15 (17 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul5 (20 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul6 (21 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul22 (19 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein el8 (29 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el21 (18 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el40 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el34 (13 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us19 (17 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us8 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal rna (1 MDa, RNA from Triticum aestivum)
- 60s ribosomal protein el18 (21 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el41 (3 kDa, Protein from Oryza sativa)
- 60s ribosomal protein ul3 (44 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el31 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el38 (8 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul15 (16 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es4 (30 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es25 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es1 (30 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el29 (6 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul13 (23 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el33 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es10 (20 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul2 (28 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul29 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul23 (16 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us13 (17 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul4 (44 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us17 (17 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us10 (14 kDa, Protein from Triticum aestivum)
- 5.8s ribosomal rna (51 kDa, RNA from Triticum aestivum)
- 60s ribosomal protein el24 (18 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us4 (22 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es28 (9 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul30 (28 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul18 (34 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el30 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us5 (29 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el37 (10 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es26 (16 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es19 (17 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el20 (21 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el14 (15 kDa, Protein from Triticum aestivum)
- Rack1 (36 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es7 (22 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el42 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us2 (33 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us9 (16 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el27 (15 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us14 (6 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el36 (12 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es6 (28 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el43 (10 kDa, Protein from Triticum aestivum)
- 5s ribosomal rna (38 kDa, RNA from Triticum aestivum)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein us3 (25 kDa, Protein from Triticum aestivum)
- 18s ribosomal rna (583 kDa, RNA from Triticum aestivum)
- 60s ribosomal protein el39 (9 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein us12 (15 kDa, Protein from Triticum aestivum)
- 4-{(2r)-2-[(1s,3s,5s)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione (281 Da, Ligand)
- 40s ribosomal protein es30 (6 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el28 (16 kDa, Protein from Triticum aestivum)
- Wheat 80s ribosome pausing on aug-stop with cycloheximide (Complex from Triticum aestivum)
- 60s ribosomal protein ul16 (24 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es8 (25 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el19 (24 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es21 (9 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es27 (9 kDa, Protein from Triticum aestivum)
- 40s ribosomal protein es24 (15 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el15 (24 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein ul14 (15 kDa, Protein from Triticum aestivum)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein ul24 (17 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el22 (14 kDa, Protein from Triticum aestivum)
- 60s ribosomal protein el13 (24 kDa, Protein from Triticum aestivum)
- Trnai (24 kDa, RNA from Triticum aestivum)
- 60s ribosomal protein el32 (15 kDa, Protein from Triticum aestivum)
- Mrna (2 kDa, RNA from Triticum aestivum)
- 40s ribosomal protein us7 (22 kDa, Protein from Triticum aestivum)
The structure of the IL-11 signalling complex, with full-length extracellular gp130
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8dpt
Q-score: 0.337
Metcalfe RD, Hanssen E, Fung KY, Aizel K, Kosasih CC, Zlatic CO, Doughty L, Morton CJ, Leis AP, Parker MW, Gooley PR, Putoczki TL, Griffin MDW
Nat Commun (2023) 14 pp. 7543-7543 [ Pubmed: 37985757 DOI: doi:10.1038/s41467-023-42754-w ]
- Interleukin-11 (18 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Il-11ra (Complex from Homo sapiens)
- Gp130 (Complex from Homo sapiens)
- Interleukin 11 signalling complex (290 kDa, Complex)
- Il-11 (Complex from Homo sapiens)
- Interleukin-11 receptor subunit alpha (32 kDa, Protein from Homo sapiens)
- Interleukin-6 receptor subunit beta (67 kDa, Protein from Homo sapiens)
H. neapolitanus carboxysomal rubisco/CsoSCA-peptide (1-50)complex
Resolution: 1.98 Å
EM Method: Single-particle
Fitted PDBs: 7smk
Q-score: 0.787
Blikstad C, Dugan EJ, Laughlin TG, Turnsek JB, Liu MD, Shoemaker SR, Vogiatzi N, Remis JP, Savage DF
PNAS (2023) 120 pp. e2308600120-e2308600120 [ DOI: doi:10.1073/pnas.2308600120 Pubmed: 37862384 ]
- Carboxysome shell carbonic anhydrase (e.c.4.2.1.1) (Complex)
- H. neapolitanus carboxysomal rubisco/csosca-peptide (1-50)complex (533 kDa, Complex)
- Ribulose bisphosphate carboxylase large chain (53 kDa, Protein from Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
- Water (18 Da, Ligand)
- Ribulose bisphosphate carboxylase small chain (12 kDa, Protein from Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
- Ribulose bisphosphate carboxylase large chain (e.c.4.1.1.39), ribulose bisphosphate carboxylase small chain (e.c.4.1.1.39) (Complex from Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
- Carboxysome shell carbonic anhydrase (5 kDa, Protein from Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
H. neapolitanus carboxysomal rubisco/CsoSCA-peptide (1-50)complex
Resolution: 2.07 Å
EM Method: Single-particle
Fitted PDBs: 7snv
Q-score: 0.771
Blikstad C, Dugan EJ, Laughlin TG, Turnsek JB, Liu MD, Shoemaker SR, Vogiatzi N, Remis JP, Savage DF
PNAS (2023) 120 pp. e2308600120-e2308600120 [ DOI: doi:10.1073/pnas.2308600120 Pubmed: 37862384 ]
- Carboxysome shell carbonic anhydrase (e.c.4.2.1.1) (Complex)
- H. neapolitanus carboxysomal rubisco/csosca-peptide (1-50)complex (533 kDa, Complex)
- Ribulose bisphosphate carboxylase large chain (53 kDa, Protein from Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
- Water (18 Da, Ligand)
- Ribulose bisphosphate carboxylase small chain (12 kDa, Protein from Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
- Ribulose bisphosphate carboxylase large chain (e.c.4.1.1.39), ribulose bisphosphate carboxylase small chain (e.c.4.1.1.39) (Complex from Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
- Carboxysome shell carbonic anhydrase (5 kDa, Protein from Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
3 A CRYO-EM STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS FERRITIN FROM TIMEPIX3 detector
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8aey
Q-score: 0.529
van Schayck JP, Zhang Y, Knoops K, Peters PJ, Ravelli RBG
Microsc Microanal (2023) [ DOI: doi:10.1093/micmic/ozac009 ]
- Ferritin bfrb (20 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Water (18 Da, Ligand)
- Mycobacterium tuberculosis ferritin (Complex from Mycobacterium tuberculosis H37Rv)
Structure of the Yeast NuA4 Histone Acetyltransferase Complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8esc
Q-score: 0.438
Zukin SA, Marunde MR, Popova IK, Soczek KM, Nogales E, Patel AB
eLife (2022) 11 [ Pubmed: 36263929 DOI: doi:10.7554/eLife.81400 ]
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf1 (112 kDa, Protein from Saccharomyces cerevisiae)
- Nua4 (1 MDa, Complex from Saccharomyces cerevisiae)
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae)
- Actin (41 kDa, Protein from Saccharomyces cerevisiae)
- Swr1-complex protein 4 (55 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Actin-related protein 4 (54 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
Cryo-electron microscopy structure of human mt-SerRS in complex with mt-tRNA(GCU-TL)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7u2b
Q-score: 0.396
Kuhle B, Hirschi M, Doerfel LK, Lander GC, Schimmel P
Nat Commun (2022) 13 pp. 5100-5100 [ DOI: doi:10.1038/s41467-022-32544-1 Pubmed: 36042193 ]
- Serine--trna ligase, mitochondrial (58 kDa, Protein from Homo sapiens)
- Rna (53-mer) (16 kDa, RNA from Homo sapiens)
- 5'-o-(n-(l-seryl)-sulfamoyl)adenosine (433 Da, Ligand)
- Human mt-serrs in complex with mt-trna(gcu-tl) and sersa (Complex from Homo sapiens)
LolCD(E171Q)E with bound AMPPNP in nanodiscs
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7v8i
Q-score: 0.345
Bei W, Luo Q, Shi H, Zhou H, Zhou M, Zhang X, Huang Y
PLoS Biol (2022) 20 pp. e3001823-e3001823 [ DOI: doi:10.1371/journal.pbio.3001823 Pubmed: 36228045 ]
- Lolcd(e171q)e with bound amppnp in nanodiscs (Complex from Escherichia coli)
- Lipoprotein-releasing system atp-binding protein lold (25 kDa, Protein from Escherichia coli K-12)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Lipoprotein-releasing system transmembrane protein lole (45 kDa, Protein from Escherichia coli K-12)
- Magnesium ion (24 Da, Ligand)
- Lipoprotein-releasing system transmembrane protein lolc (43 kDa, Protein from Escherichia coli K-12)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7ucg
Q-score: 0.411
Barnes CO, Schoofs T, Gnanapragasam PNP, Golijanin J, Huey-Tubman KE, Gruell H, Schommers P, Suh-Toma N, Lee YE, Cetrulo Lorenzi JC, Piechocka-Trocha A, Scheid JF, West Jr AP, Walker BD, Seaman MS, Klein F, Nussenzweig MC, Bjorkman PJ
Sci Adv (2022) 8 pp. eabp8155-eabp8155 [ Pubmed: 35960796 DOI: doi:10.1126/sciadv.abp8155 ]
- Complex of du422 sosip trimer bound to 10-1074 and bg24 fab fragments (650 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 10-1074 fab heavy chain (26 kDa, Protein from Homo sapiens)
- Bg24 light chain (21 kDa, Protein from Homo sapiens)
- Bg24 cdrh2-v2 fab heavy chain (25 kDa, Protein from Homo sapiens)
- 10-1074 light chain (23 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein gp160 (56 kDa, Protein from Human immunodeficiency virus 1)