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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:"30S ribosomal protein S4" AND structure_determination_method:"singleparticle" AND author_name:"Wilson DN" AND citation_journal_name:"NAT CHEM BIOL"

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EMD-15488

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Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome

Release date: March 8, 2023
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8akn
Q-score: 0.647

Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN

Nat Chem Biol (2023) 19 pp. 1072-1081 [ DOI: doi:10.1038/s41589-023-01293-7 Pubmed: 36997646 ]

Sample:

30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BW25113)
Phenylalanine-trna (24 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli BW25113)
Mrna (2 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli BW25113)
Peptide chain release factor rf1 (40 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
2-acetamido-2-deoxy-alpha-d-galactopyranose (221 Da, Ligand)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BW25113)
Drosocin1 (2 kDa, Protein from Drosophila melanogaster)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BW25113)
Spermine (202 Da, Ligand)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BW25113)
Isoleucine-trna (24 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli BW25113)
Zinc ion (65 Da, Ligand)
5s ribosomal rna (38 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli BW25113)
23s ribosomal rna (941 kDa, RNA from Escherichia coli BW25113)
Water (18 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BW25113)
Magnesium ion (24 Da, Ligand)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BW25113)
Cryo-em structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome (2 MDa, Complex from Escherichia coli BW25113)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli BW25113)
16s ribosomal rna (497 kDa, RNA from Escherichia coli BW25113)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)

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EMD-15523

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Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome

Release date: March 8, 2023
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8am9
Q-score: 0.594

Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN

Nat Chem Biol (2023) 19 pp. 1072-1081 [ DOI: doi:10.1038/s41589-023-01293-7 Pubmed: 36997646 ]

Sample:

23s ribosomal rna (941 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli BW25113)
16s ribosomal rna (497 kDa, RNA from Escherichia coli BW25113)
30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli BW25113)
Mrna (3 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli BW25113)
Cryo-em structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome (2 MDa, Complex from Escherichia coli K-12)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BW25113)
Initiator trna (24 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BW25113)
Magnesium ion (24 Da, Ligand)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BW25113)
5s ribosomal rna (38 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BW25113)
Spermine (202 Da, Ligand)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BW25113)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli BW25113)
Leucine trna (27 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BW25113)
2-acetamido-2-deoxy-alpha-d-galactopyranose (221 Da, Ligand)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli BW25113)
Drosocin1 (2 kDa, Protein from Drosophila melanogaster)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BW25113)
Water (18 Da, Ligand)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli BW25113)

[Show more]

EMD-10705

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Cryo-EM structure of an Escherichia coli 70S ribosome in complex with antibiotic TetracenomycinX

Release date: July 1, 2020
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 6y69
Q-score: 0.486

Osterman IA, Wieland M, Maviza TP, Lashkevich KA, Lukianov DA, Komarova ES, Zakalyukina YV, Buschauer R, Shiriaev DI, Leyn SA, Zlamal JE, Biryukov MV, Skvortsov DA, Tashlitsky VN, Polshakov VI, Cheng J, Polikanov YS, Bogdanov AA, Osterman AL, Dmitriev SE, Beckmann R, Dontsova OA, Wilson DN, Sergiev PV

Nat Chem Biol (2020) 16 pp. 1071-1077 [ DOI: doi:10.1038/s41589-020-0578-x Pubmed: 32601485 ]

Sample:

Cryo-em structure of the antibiotic tetracenomycinx bound to the escherichia coli 70s ribosome (2 MDa, Complex from Escherichia coli K-12)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
16s ribosomal rna (498 kDa, RNA from Escherichia coli (strain K12))
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli (strain K12))
E-site trna (24 kDa, RNA from Escherichia coli (strain K12))
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l9 (8 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli (strain K12))
5s ribosomal rna (38 kDa, RNA from Escherichia coli (strain K12))
50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s21 (7 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
Tetracenomycin x (486 Da, Ligand)
30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l15 (14 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 l36 (4 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli (strain K12))
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s7 (17 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
23s ribosomal rna (941 kDa, RNA from Escherichia coli (strain K12))
Ribosome hibernation promoting factor (10 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))

[Show more]

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Display: Statistics

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Select database:

EMDB [3]

Format:

Select the script type:

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