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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:

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Tissue biology and disease modelling

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Structural biology

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sample_name:"50S ribosomal protein L33 1" AND natural_source_ncbi_code:"224308" AND author_name:"Beckert B"

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EMD-19638

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YlmH bound to PtRNA-50S

Release date: June 12, 2024
Resolution: 1.96 Å
EM Method: Single-particle
Fitted PDBs: 8s1p

Takada H, Paternoga H, Fujiwara K, Nakamoto JA, Park EN, Dimitrova-Paternoga L, Beckert B, Saarma M, Tenson T, Buskirk AR, Atkinson GC, Chiba S, Wilson DN, Hauryliuk V

Nucleic Acids Res (2024) [ Pubmed: 38811035 DOI: doi:10.1093/nar/gkae399 ]

Sample:

Large ribosomal subunit protein bl20 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein ul6 (19 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal subunit with stalled p-trna-nascent chain, bound by ylmh (Complex from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Potassium ion (39 Da, Ligand)
Chloramphenicol (323 Da, Ligand)
50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Zinc ion (65 Da, Ligand)
Large ribosomal subunit protein ul23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein bl27 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein ul30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Putative rna-binding protein ylmh (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Water (18 Da, Ligand)
50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
P-trna (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
Magnesium ion (24 Da, Ligand)
Nascent chain (358 Da, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l31 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
23s rrna (949 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
5s rrna (36 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)

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EMD-19641

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YlmH bound to stalled 50S subunits with RqcH and PtRNA

Release date: June 12, 2024
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8s1u

Takada H, Paternoga H, Fujiwara K, Nakamoto JA, Park EN, Dimitrova-Paternoga L, Beckert B, Saarma M, Tenson T, Buskirk AR, Atkinson GC, Chiba S, Wilson DN, Hauryliuk V

Nucleic Acids Res (2024) [ Pubmed: 38811035 DOI: doi:10.1093/nar/gkae399 ]

Sample:

Large ribosomal subunit protein bl20 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein ul6 (19 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Rqc2 homolog rqch (65 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal subunit with stalled p-trna-nascent chain, bound by ylmh (Complex from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein ul23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein bl27 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Putative rna-binding protein ylmh (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein ul30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
P-trna (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l31 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
23s rrna (949 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
5s rrna (36 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)

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EMD-18332

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B. subtilis ApdA-stalled ribosomal complex

Release date: March 20, 2024
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8qcq
Q-score: 0.61

Morici M, Gabrielli S, Fujiwara K, Paternoga H, Beckert B, Bock LV, Chiba S, Wilson DN

Nat Commun (2024) 15 pp. 2432-2432 [ Pubmed: 38503735 DOI: doi:10.1038/s41467-024-46761-3 ]

Sample:

Large ribosomal subunit protein bl20 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Small ribosomal subunit protein us7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein ul6 (19 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Small ribosomal subunit protein us3 (23 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s11 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
23s rrna (948 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Mrna (1 kDa, RNA from Amycolatopsis japonica)
30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l16 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
5s rrna (38 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
16s rrna (503 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein bl31-a (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s19 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Potassium ion (39 Da, Ligand)
Proline (115 Da, Ligand)
50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Zinc ion (65 Da, Ligand)
Large ribosomal subunit protein ul23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Pro-trna (24 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein bl27 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Large ribosomal subunit protein ul30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Water (18 Da, Ligand)
30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s13 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Apda nascent chain (970 Da, Protein from Amycolatopsis japonica)
30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
B. subtilis apda-stalled ribosomal complex (Complex from Amycolatopsis japonica)
50s ribosomal protein l24 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)

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EMD-3656

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Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.

Release date: June 14, 2017
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 5njt
Q-score: 0.381

Beckert B, Abdelshahid M, Schafer H, Steinchen W, Arenz S, Berninghausen O, Beckmann R, Bange G, Turgay K, Wilson DN

EMBO J (2017) 36 pp. 2061-2072 [ DOI: doi:10.15252/embj.201696189 Pubmed: 28468753 ]

Sample:

50s ribosomal protein l20 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l5 (20 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s2 (25 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l34 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Ribosome hibernation promotion factor (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
5s ribosomal rna (36 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s18 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l6 (19 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l33 1 (5 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s3 (23 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l27 (8 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s10 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s8 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s16 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l3 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l18 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l19 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s13 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s6 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l14 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l17 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l29 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
16s ribosomal rna (500 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l31 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l32 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l30 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l2 (30 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l28 (6 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s12 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l35 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s15 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l36 (4 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
Structure of the bacillus subtilis hibernating 100s ribosome reveals the basis for 70s dimerization (Complex from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s5 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l10 (13 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s14 (7 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l22 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s17 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
23s ribosomal rna (947 kDa, RNA from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s9 (14 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s11 (12 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l16 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l4 (22 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l15 (15 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s20 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s19 (9 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
30s ribosomal protein s7 (17 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l24 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l13 (16 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l23 (10 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)
50s ribosomal protein l21 (11 kDa, Protein from Bacillus subtilis subsp. subtilis str. 168)

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