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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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primary_citation_author:"Vaitkevicius K" AND xref_links:"pdbekb" AND natural_source_ncbi_code:"169963"

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EMD-15161

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Cryo-EM structure of HflXr bound to the Listeria monocytogenes 50S ribosomal subunit.

Release date: Nov. 2, 2022
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8a57
Q-score: 0.579

Koller TO, Turnbull KJ, Vaitkevicius K, Crowe-McAuliffe C, Roghanian M, Bulvas O, Nakamoto JA, Kurata T, Julius C, Atkinson GC, Johansson J, Hauryliuk V, Wilson DN

Nucleic Acids Res (2022) 50 pp. 11285-11300 [ Pubmed: 36300626 DOI: doi:10.1093/nar/gkac934 ]

Sample:

50s ribosomal protein l3 (22 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l23 (10 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l34 (5 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l28 (7 kDa, Protein from Listeria monocytogenes EGD-e)
Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
50s ribosomal protein l36 (4 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l31 type b (9 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l5 (20 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l2 (30 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l33 1 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l13 (16 kDa, Protein from Listeria monocytogenes EGD-e)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l35 (7 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l27 (10 kDa, Protein from Listeria monocytogenes EGD-e)
Zinc ion (65 Da, Ligand)
1,4-diaminobutane (88 Da, Ligand)
Spermidine (145 Da, Ligand)
50s ribosomal protein l6 (19 kDa, Protein from Listeria monocytogenes EGD-e)
Gtpase hflx (47 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l30 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l17 (15 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l24 (11 kDa, Protein from Listeria monocytogenes EGD-e)
Hflxr bound to the listeria monocytogenes 50s ribosomal subunit (1 MDa, Complex from Listeria monocytogenes E)
50s ribosomal protein l4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l21 (11 kDa, Protein from Listeria monocytogenes EGD-e)
Magnesium ion (24 Da, Ligand)
23s ribosomal rna (950 kDa, RNA from Listeria monocytogenes EGD-e)
5s ribosomal rna (36 kDa, RNA from Listeria monocytogenes EGD-e)
50s ribosomal protein l19 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l22 (12 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l32-2 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l11 (14 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l20 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l16 (16 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l15 (15 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l29 (7 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l14 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l18 (13 kDa, Protein from Listeria monocytogenes EGD-e)

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EMD-15175

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Cryo-EM structure of Lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit.

Release date: Nov. 2, 2022
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8a5i
Q-score: 0.638

Koller TO, Turnbull KJ, Vaitkevicius K, Crowe-McAuliffe C, Roghanian M, Bulvas O, Nakamoto JA, Kurata T, Julius C, Atkinson GC, Johansson J, Hauryliuk V, Wilson DN

Nucleic Acids Res (2022) 50 pp. 11285-11300 [ Pubmed: 36300626 DOI: doi:10.1093/nar/gkac934 ]

Sample:

Lincomycin (406 Da, Ligand)
50s ribosomal protein l27 (10 kDa, Protein from Listeria monocytogenes EGD-e)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l3 (22 kDa, Protein from Listeria monocytogenes EGD-e)
23s ribosomal rna (950 kDa, RNA from Listeria monocytogenes EGD-e)
1,4-diaminobutane (88 Da, Ligand)
50s ribosomal protein l36 (4 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l15 (15 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l23 (10 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l29 (7 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l31 type b (9 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l18 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l6 (19 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l34 (5 kDa, Protein from Listeria monocytogenes EGD-e)
Magnesium ion (24 Da, Ligand)
Spermidine (145 Da, Ligand)
50s ribosomal protein l24 (11 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l13 (16 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l32-2 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l17 (15 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l5 (20 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l22 (12 kDa, Protein from Listeria monocytogenes EGD-e)
5s ribosomal rna (36 kDa, RNA from Listeria monocytogenes EGD-e)
50s ribosomal protein l20 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l35 (7 kDa, Protein from Listeria monocytogenes EGD-e)
Lincomycin bound to the listeria monocytogenes 50s ribosomal subunit. (1 MDa, Complex from Listeria monocytogenes E)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l2 (30 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l19 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l28 (7 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l14 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l21 (11 kDa, Protein from Listeria monocytogenes EGD-e)
Water (18 Da, Ligand)
50s ribosomal protein l30 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l16 (16 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l33 1 (6 kDa, Protein from Listeria monocytogenes EGD-e)

[Show more]

EMD-15204

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Cryo-EM structure of Listeria monocytogenes 50S ribosomal subunit.

Release date: Nov. 2, 2022
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8a63
Q-score: 0.503

Koller TO, Turnbull KJ, Vaitkevicius K, Crowe-McAuliffe C, Roghanian M, Bulvas O, Nakamoto JA, Kurata T, Julius C, Atkinson GC, Johansson J, Hauryliuk V, Wilson DN

Nucleic Acids Res (2022) 50 pp. 11285-11300 [ Pubmed: 36300626 DOI: doi:10.1093/nar/gkac934 ]

Sample:

50s ribosomal protein l3 (22 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l23 (10 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l34 (5 kDa, Protein from Listeria monocytogenes EGD-e)
Listeria monocytogenes 50s ribosomal subunit. (1 MDa, Complex from Listeria monocytogenes EGD-e)
50s ribosomal protein l28 (7 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l36 (4 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l31 type b (9 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l5 (20 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l2 (30 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l33 1 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l13 (16 kDa, Protein from Listeria monocytogenes EGD-e)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l35 (7 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l27 (10 kDa, Protein from Listeria monocytogenes EGD-e)
Zinc ion (65 Da, Ligand)
1,4-diaminobutane (88 Da, Ligand)
Spermidine (145 Da, Ligand)
50s ribosomal protein l6 (19 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l30 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l17 (15 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l24 (11 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l21 (11 kDa, Protein from Listeria monocytogenes EGD-e)
Magnesium ion (24 Da, Ligand)
23s ribosomal rna (950 kDa, RNA from Listeria monocytogenes EGD-e)
5s ribosomal rna (36 kDa, RNA from Listeria monocytogenes EGD-e)
50s ribosomal protein l19 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l22 (12 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l32-2 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l20 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l16 (16 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l15 (15 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l29 (7 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l14 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l18 (13 kDa, Protein from Listeria monocytogenes EGD-e)

[Show more]

EMD-12334

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VgaL, an antibiotic resistance ABCF, in complex with 70S ribosome from Listeria monocytogenes

Release date: May 5, 2021
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7nhn
Q-score: 0.534

Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN

Nat Commun (2021) 12 pp. 3577-3577 [ Pubmed: 34117249 DOI: doi:10.1038/s41467-021-23753-1 ]

Sample:

50s ribosomal protein l3 (22 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l23 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s7 (17 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l34 (5 kDa, Protein from Listeria monocytogenes EGD-e)
Vgal in complex with 70s ribosome, mrna, and distorted p-trna from listeria monocytogenes (2 MDa, Complex from Listeria monocytogenes EGD-e)
50s ribosomal protein l28 (7 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s19 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s8 (14 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s12 (15 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s14 type z (7 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s15 (10 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l36 (4 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l31 type b (9 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l5 (20 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s17 (10 kDa, Protein from Listeria monocytogenes EGD-e)
Rna (5'-r(p*gp*ap*gp*gp*up*np*np*np*np*np*np*ap*up*g)-3') (3 kDa, RNA from Listeria monocytogenes EGD-e)
30s ribosomal protein s2 (28 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l2 (30 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l33 1 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l13 (16 kDa, Protein from Listeria monocytogenes EGD-e)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l27 (10 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l35 (7 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
Zinc ion (65 Da, Ligand)
Trna-fmet (24 kDa, RNA from Listeria monocytogenes EGD-e)
30s ribosomal protein s10 (11 kDa, Protein from Listeria monocytogenes EGD-e)
Spermidine (145 Da, Ligand)
Lmo0919 protein (64 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s5 (17 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s9 (14 kDa, Protein from Listeria monocytogenes EGD-e)
Adenosine-5'-triphosphate (507 Da, Ligand)
30s ribosomal protein s18 (9 kDa, Protein from Listeria monocytogenes EGD-e)
16s rrna (499 kDa, RNA from Listeria monocytogenes EGD-e)
50s ribosomal protein l6 (19 kDa, Protein from Listeria monocytogenes EGD-e)
23s rrna (949 kDa, RNA from Listeria monocytogenes EGD-e)
30s ribosomal protein s11 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l17 (15 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l24 (11 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l30 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s6 (11 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l21 (11 kDa, Protein from Listeria monocytogenes EGD-e)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l19 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l22 (12 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l32-2 (6 kDa, Protein from Listeria monocytogenes EGD-e)
5s rrna (36 kDa, RNA from Listeria monocytogenes EGD-E)
50s ribosomal protein l20 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l16 (16 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s16 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s3 (24 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l15 (15 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l29 (7 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l14 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l18 (13 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s13 (13 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s20 (9 kDa, Protein from Listeria monocytogenes EGD-e)

[Show more]

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EMDB [4]

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