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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

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offer vital services to scientists in the member states

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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 current_status:"REL" AND resolution:[2 TO 3} AND author_name:"Dn"

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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 [ Pubmed: 34294725 DOI: doi:10.1038/s41467-021-24674-9 ]

Sample:

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

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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 [ DOI: doi:10.1038/s41467-021-23753-1 Pubmed: 34117249 ]

Sample:

30s ribosomal protein s4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
16s rrna (499 kDa, RNA from Listeria monocytogenes EGD-e)
30s ribosomal protein s16 (10 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l33 1 (6 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s17 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s11 (13 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)
30s ribosomal protein s3 (24 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l17 (15 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s9 (14 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l30 (6 kDa, Protein from Listeria monocytogenes EGD-e)
Trna-fmet (24 kDa, RNA from Listeria monocytogenes EGD-e)
50s ribosomal protein l28 (7 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)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l20 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l3 (22 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l14 (13 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)
50s ribosomal protein l5 (20 kDa, Protein from Listeria monocytogenes EGD-e)
Adenosine-5'-triphosphate (507 Da, Ligand)
50s ribosomal protein l27 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s10 (11 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 l29 (7 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s20 (9 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l13 (16 kDa, Protein from Listeria monocytogenes EGD-e)
Spermidine (145 Da, Ligand)
50s ribosomal protein l34 (5 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l22 (12 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s15 (10 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l21 (11 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l2 (30 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l35 (7 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l19 (13 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s12 (15 kDa, Protein from Listeria monocytogenes EGD-e)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l15 (15 kDa, Protein from Listeria monocytogenes EGD-e)
Lmo0919 protein (64 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l16 (16 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s13 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l24 (11 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s2 (28 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l31 type b (9 kDa, Protein from Listeria monocytogenes EGD-e)
23s rrna (949 kDa, RNA from Listeria monocytogenes EGD-e)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s7 (17 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s19 (10 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l23 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s6 (11 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l36 (4 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s14 type z (7 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s18 (9 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s8 (14 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s5 (17 kDa, Protein from Listeria monocytogenes EGD-e)

[Show more]

EMD-11889

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Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO

Release date: Dec. 9, 2020
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7as8
Q-score: 0.497

Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V

Mol Cell (2021) 81 pp. 115- [ DOI: doi:10.1016/j.molcel.2020.11.002 Pubmed: 33259810 ]

Sample:

Rqc2 homolog rqch (68 kDa, Protein from Bacillus subtilis (strain 168))
Uncharacterized protein yabo (9 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis (strain 168))
23s rrna (949 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal subunit in complex with rqch, p-trna, and yabo/rqcp (1 MDa, Complex)
50s ribosomal protein l23 (10 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l6 (19 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l27 (10 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l11 (14 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l30 (6 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l10 (18 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis (strain 168))
Trna-ala-1-1 (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis (strain 168))
5s rrna (38 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal protein l20 (13 kDa, Protein from Bacillus subtilis (strain 168))
50s ribosomal subunit in complex with p-trna, and yabo/rqcp (Complex from Bacillus subtilis (strain 168))
Rqch (Complex from Bacillus subtilis (strain 168))

[Show more]

EMD-11914

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Ribosome-associated quality control complex from Bacillus subtilis, state D. Large ribosomal subunit in complex with P-tRNA and RqcP/YabO.

Release date: Dec. 9, 2020
Resolution: 2.6 Å
EM Method: Single-particle

Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V

Mol Cell (2021) 81 pp. 115-126.e7 [ DOI: doi:10.1016/j.molcel.2020.11.002 Pubmed: 33259810 ]

Sample:

50s ribosomal subunit in complex with p-trna and rqcp/yabo. (1 MDa, Complex from Bacillus subtilis subsp. subtilis str. 168)

EMD-11915

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Bacillus subtilis ribosome-associated quality control complex state B*, derived from RqcH affinity purification.

Release date: Dec. 9, 2020
Resolution: 2.9 Å
EM Method: Single-particle

Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V

Mol Cell (2021) 81 pp. 115-126.e7 [ DOI: doi:10.1016/j.molcel.2020.11.002 Pubmed: 33259810 ]

Sample:

50s ribosomal subunit in complex with p-trna, yabo/rqcp, and partially dissociated rqch (1 MDa, Complex from Bacillus subtilis subsp. subtilis str. 168)

EMD-11918

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Bacillus subtilis ribosome-associated quality control complex, state D, derived from RqcP/YabO affinity purification.

Release date: Dec. 9, 2020
Resolution: 2.6 Å
EM Method: Single-particle

Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V

Mol Cell (2021) 81 pp. 115-126.e7 [ DOI: doi:10.1016/j.molcel.2020.11.002 Pubmed: 33259810 ]

Sample:

50s in complex with p-trna and rqcp/yabo (1 MDa, Complex from Bacillus subtilis subsp. subtilis str. 168)

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