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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:"Stalled ribosome" AND xref_links:"alphafold" AND xref_links:"empiar"

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EMD-18534

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Structure of SecM-stalled Escherichia coli 70S ribosome

Release date: March 20, 2024
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 8qoa
Q-score: 0.652

Gersteuer F, Morici M, Gabrielli S, Fujiwara K, Safdari HA, Paternoga H, Bock LV, Chiba S, Wilson DN

Nat Commun (2024) 15 pp. 2431-2431 [ DOI: doi:10.1038/s41467-024-46762-2 Pubmed: 38503753 ]

Sample:

Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein bl31a (7 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli BW25113)
16s rrna (499 kDa, RNA from Escherichia coli BW25113)
Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli BW25113)
Potassium ion (39 Da, Ligand)
Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul23 (11 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli BW25113)
23s rrna (941 kDa, RNA from Escherichia coli BW25113)
Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli BW25113)
A-site trna-pro (24 kDa, RNA from Escherichia coli BW25113)
Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli BW25113)
5s rrna (38 kDa, RNA from Escherichia coli BW25113)
Large ribosomal subunit protein bl33 (6 kDa, Protein from Escherichia coli BW25113)
Water (18 Da, Ligand)
Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli BW25113)
Secretion monitor (3 kDa, Protein from Escherichia coli BW25113)
E-site trna (589 Da, RNA from Escherichia coli BW25113)
Magnesium ion (24 Da, Ligand)
P-site trna-gly (24 kDa, RNA from Escherichia coli BW25113)
Large ribosomal subunit protein bl28 (9 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
Zinc ion (65 Da, Ligand)
Mrna (2 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli BW25113)
Proline (115 Da, Ligand)
Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli BW25113)
Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli BW25113)
Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
Secm-stalled ribosome complex (Complex from Escherichia coli BW25113)
Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli BW25113)

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EMD-10906

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Structure of the P+9 ArfB-ribosome complex in the post-hydrolysis state

Release date: Aug. 19, 2020
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 6yss
Q-score: 0.613

Chan KH, Petrychenko V, Mueller C, Maracci C, Holtkamp W, Wilson DN, Fischer N, Rodnina MV

Nat Commun (2020) 11 pp. 4106-4106 [ Pubmed: 32796827 DOI: doi:10.1038/s41467-020-17853-7 ]

Sample:

30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 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 l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 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 l18 (12 kDa, Protein from Escherichia coli)
Post-hydrolysis state of e. coli ribosome p+9 70s-arfb-api137-trnaphe-mrna complex (2 MDa, Complex)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
Api137 (1 kDa, Protein from Apis mellifera)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
Post-hydrolysis state of e. coli ribosome p+9 70s-arfb-api137-trnaphe-mrna complex (Complex from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
Alternative stalled-ribosome rescue factor b (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
16s ribosomal rna (499 kDa, RNA from Escherichia coli)
Magnesium ion (24 Da, Ligand)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
Post-hydrolysis state of e. coli ribosome p+9 70s-arfb-api137-trnaphe-mrna complex (Complex from Apis mellifera)
5s ribosomal rna (38 kDa, RNA from Escherichia coli)
Sodium ion (22 Da, Ligand)
23s ribosomal rna (941 kDa, RNA from Escherichia coli)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
P-site trnaphe (24 kDa, RNA from Escherichia coli)
Mrna (4 kDa, RNA from Escherichia coli)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)

[Show more]

EMD-10907

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Structure of the P+9 ArfB-ribosome complex with P/E hybrid tRNA in the post-hydrolysis state

Release date: Aug. 19, 2020
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6yst
Q-score: 0.471

Chan KH, Petrychenko V, Mueller C, Maracci C, Holtkamp W, Wilson DN, Fischer N, Rodnina MV

Nat Commun (2020) 11 pp. 4106-4106 [ Pubmed: 32796827 DOI: doi:10.1038/s41467-020-17853-7 ]

Sample:

30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
Post-hydrolysis state of e. coli ribosome p+9 70s-arfb-api137-trnaphe-mrna complex with p/e hybrid trna (Complex from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 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 l18 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
Api137 (1 kDa, Protein from Apis mellifera)
P/e-site trnaphe (24 kDa, RNA from Escherichia coli)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
Post-hydrolysis state of e. coli ribosome p+9 70s-arfb-api137-trnaphe-mrna complex with p/e hybrid trna (2 MDa, Complex)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
Alternative stalled-ribosome rescue factor b (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
16s ribosomal rna (499 kDa, RNA from Escherichia coli)
Magnesium ion (24 Da, Ligand)
Post-hydrolysis state of e. coli ribosome p+9 70s-arfb-api137-trnaphe-mrna complex with p/e hybrid trna (Complex from Apis mellifera)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
5s ribosomal rna (38 kDa, RNA from Escherichia coli)
Sodium ion (22 Da, Ligand)
23s ribosomal rna (941 kDa, RNA from Escherichia coli)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
Mrna (4 kDa, RNA from Escherichia coli)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)

[Show more]

EMD-10908

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Structure of the P+0 ArfB-ribosome complex in the post-hydrolysis state

Release date: Aug. 19, 2020
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6ysu
Q-score: 0.446

Chan KH, Petrychenko V, Mueller C, Maracci C, Holtkamp W, Wilson DN, Fischer N, Rodnina MV

Nat Commun (2020) 11 pp. 4106-4106 [ Pubmed: 32796827 DOI: doi:10.1038/s41467-020-17853-7 ]

Sample:

30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 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 l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
Post-hydrolysis state of e. coli ribosome p+0 70s-arfb-api137-trnaphe-mrna complex (Complex from Apis mellifera)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
Api137 (1 kDa, Protein from Apis mellifera)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
Post-hydrolysis state of e. coli ribosome p+0 70s-arfb-api137-trnaphe-mrna complex (2 MDa, Complex)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
Alternative stalled-ribosome rescue factor b (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
Post-hydrolysis state of e. coli ribosome p+0 70s-arfb-api137-trnaphe-mrna complex (Complex from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
16s ribosomal rna (499 kDa, RNA from Escherichia coli)
Magnesium ion (24 Da, Ligand)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
5s ribosomal rna (38 kDa, RNA from Escherichia coli)
Sodium ion (22 Da, Ligand)
23s ribosomal rna (941 kDa, RNA from Escherichia coli)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
P-site trnaphe (24 kDa, RNA from Escherichia coli)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
Rna (5'-r(p*ap*up*gp*up*up*c)-3') (4 kDa, RNA from Escherichia coli)

[Show more]

Sort by: Download

Showing 1 - 4 of 4. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [4]

Format:

Select the script type:

Shell (Unix-based) Batch (Windows-based)

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