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EMBL

was set up in 1974 as Europe’s flagship laboratory for the life sciences – an intergovernmental organisation with more than 80 independent research groups covering the spectrum of molecular biology:

Research:

perform basic research in molecular biology

Services:

offer vital services to scientists in the member states

Training

scientists, students and visitors at all levels

Transfer

and development of technology

Develop

new instruments and methods

Integrating

life science research in Europe

More about EMBL

Six sites

represent EMBL in Europe.

Barcelona

Tissue biology and disease modelling

Grenoble

Structural biology

Hamburg

Structural biology

Heidelberg

Main laboratory

Hinxton

EMBL-EBI: European Bioinformatics Institute

Rome

Epigenetics and neurobiology

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sample_name:"P-tRNA" AND author_name:"Arenz S"

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EMD-15905

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Cryo-EM structure of the E.coli 70S ribosome in complex with the antibiotic Myxovalargin B.

Release date: Jan. 25, 2023
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8b7y
Q-score: 0.556

Koller TO, Scheid U, Kosel T, Herrmann J, Krug D, Boshoff HIM, Beckert B, Evans JC, Schlemmer J, Sloan B, Weiner DM, Via LE, Moosa A, Ioerger TR, Graf M, Zinshteyn B, Abdelshahid M, Nguyen F, Arenz S, Gille F, Siebke M, Seedorf T, Plettenburg O, Green R, Warnke AL, Ullrich J, Warrass R, Barry 3rd CE, Warner DF, Mizrahi V, Kirschning A, Wilson DN, Muller R

J Am Chem Soc (2023) 145 pp. 851-863 [ DOI: doi:10.1021/jacs.2c08816 Pubmed: 36603206 ]

Sample:

50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli K-12)
16s ribosomal rna (496 kDa, RNA from Escherichia coli K-12)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli K-12)
5s ribosomal rna (38 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli K-12)
N-formylmethionine (177 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli K-12)
Cryo-em structure of the e.coli 70s ribosome in complex with the antibiotic myxovalargin b. (2 MDa, Complex from Escherichia coli BW25113)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K-12)
P-trna fmet (24 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli K-12)
Myxovalargin b (1 kDa, Protein from Myxococcus fulvus)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli K-12)
Spermidine (145 Da, Ligand)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli K-12)
23s ribosomal rna (941 kDa, RNA from Escherichia coli K-12)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli K-12)
Water (18 Da, Ligand)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli K-12)
Magnesium ion (24 Da, Ligand)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli K-12)
Messenger rna (935 Da, RNA from Escherichia coli K-12)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli K-12)

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EMD-12574

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Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal complex with A and P-tRNA

Release date: Aug. 11, 2021
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7nsp
Q-score: 0.448

Beckert B, Leroy EC, Sothiselvam S, Bock LV, Svetlov MS, Graf M, Arenz S, Abdelshahid M, Seip B, Grubmuller H, Mankin AS, Innis CA, Vazquez-Laslop N, Wilson DN

Nat Commun (2021) 12 pp. 4466-4466 [ DOI: doi:10.1038/s41467-021-24674-9 Pubmed: 34294725 ]

Sample:

50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
23s rrna (941 kDa, RNA from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
P-trna (leu) (28 kDa, RNA from Escherichia coli)
50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
Ermdl (877 Da, Protein from Escherichia coli)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
16s rrna (499 kDa, RNA from Escherichia coli)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli)
A-trna (arg) (24 kDa, RNA from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
Erythromycin a (733 Da, Ligand)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli)
Structure of ermdl-erythromycin-stalled 70s e. coli ribosomal complex with a and p-trna (Complex from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
Mrna (1 kDa, RNA from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)

[Show more]

EMD-12573

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Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal complex with P-tRNA

Release date: July 14, 2021
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7nso
Q-score: 0.551

Beckert B, Leroy EC, Sothiselvam S, Bock LV, Svetlov MS, Graf M, Arenz S, Abdelshahid M, Seip B, Grubmuller H, Mankin AS, Innis CA, Vazquez-Laslop N, Wilson DN

Nat Commun (2021) 12 pp. 4466-4466 [ DOI: doi:10.1038/s41467-021-24674-9 Pubmed: 34294725 ]

Sample:

50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
Structure of ermdl-erythromycin-stalled 70s e. coli ribosomal complex with p-trna (Complex from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
Ermdl (877 Da, Protein from Escherichia coli)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
Ptrna-leu (28 kDa, RNA from Escherichia coli)
30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
16s rrna (1540-mer) (499 kDa, RNA from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
Erythromycin a (733 Da, Ligand)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
23s rrna (2903-mer) (941 kDa, RNA from Escherichia coli)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli)
Mrna (872 Da, RNA from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)

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EMD-12575

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Structure of ErmDL-Telithromycin-stalled 70S E. coli ribosomal complex with A and P-tRNA

Release date: July 14, 2021
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7nsq
Q-score: 0.52

Beckert B, Leroy EC, Sothiselvam S, Bock LV, Svetlov MS, Graf M, Arenz S, Abdelshahid M, Seip B, Grubmuller H, Mankin AS, Innis CA, Vazquez-Laslop N, Wilson DN

Nat Commun (2021) 12 pp. 4466-4466 [ DOI: doi:10.1038/s41467-021-24674-9 Pubmed: 34294725 ]

Sample:

50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
Telithromycin (812 Da, Ligand)
23s rrna (941 kDa, RNA from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
Structure of ermdl-erythromycin-stalled 70s e. coli ribosomal complex with p-trna (Complex from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
Ermdl (877 Da, Protein from Escherichia coli)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
16s rrna (499 kDa, RNA from Escherichia coli)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
Ptrna (leu) (28 kDa, RNA from Escherichia coli)
30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
Mrna (1 kDa, RNA from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
Atrna (arg) (24 kDa, RNA from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)

[Show more]

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EMDB [4]

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