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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:"SPERMINE" AND film_detector_model:"GATAN K3 (6K X 4K)" AND author_orcid:"0000-0001-5965-7902"

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EMD-28254

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Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates

Release date: May 31, 2023
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 8emm
Q-score: 0.678

Watson ZL, Knudson IJ, Ward FR, Miller SJ, Cate JHD, Schepartz A, Abramyan AM

Nat Chem (2023) 15 pp. 913-921 [ Pubmed: 37308707 DOI: doi:10.1038/s41557-023-01226-w ]

Sample:

Potassium ion (39 Da, Ligand)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
70s ribosome complex with mrna, a- and p-site met-nh-trnas (Complex from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
23s rrna (941 kDa, RNA from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
Met-nh-trna (24 kDa, RNA from Escherichia coli)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
Spermidine (145 Da, Ligand)
Paromomycin (615 Da, Ligand)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Methionine (149 Da, Ligand)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
Spermine (202 Da, Ligand)
Mrna (9 kDa, RNA from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
Water (18 Da, Ligand)
Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
16s rrna (499 kDa, RNA from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)

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EMD-28165

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E. coli 70S ribosome with A-loop mutations U2554C and U2555C (Composite Map)

Release date: Feb. 1, 2023
Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8eiu
Q-score: 0.658

Nissley AJ, Penev PI, Watson ZL, Banfield JF, Cate JHD

Nucleic Acids Res (2023) 51 pp. 1880-1894 [ Pubmed: 36660825 DOI: doi:10.1093/nar/gkac1273 ]

Sample:

30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
Methionine (149 Da, Ligand)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
E. coli 70s ribosome with a-loop mutations u2554c and u2555c (850 kDa, Complex from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
Mrna (8 kDa, RNA from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
Spermine (202 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
50s subunit (Complex from Escherichia coli)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
30s subunit (Complex from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
Spermidine (145 Da, Ligand)
16s rrna (499 kDa, RNA from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
23s rrna (941 kDa, RNA from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) (346 Da, Ligand)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
Water (18 Da, Ligand)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Trna-fmet (24 kDa, RNA from Escherichia coli)
Paromomycin (615 Da, Ligand)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)

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EMD-22586

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Structure of the Bacterial Ribosome at 2 Angstrom Resolution (composite structure)

Release date: Sept. 23, 2020
Resolution: 1.98 Å
EM Method: Single-particle
Fitted PDBs: 7k00
Q-score: 0.677

Watson ZL, Ward FR, Meheust R, Ad O, Schepartz A, Banfield JF, Cate JH

eLife (2020) 9 [ DOI: doi:10.7554/eLife.60482 Pubmed: 32924932 ]

Sample:

50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
23s rrna (941 kDa, RNA from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
P-site trna-fmet (24 kDa, RNA from Escherichia coli)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
Paromomycin (615 Da, Ligand)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
A-site trna-val (24 kDa, RNA from Escherichia coli)
Magnesium ion (24 Da, Ligand)
Spermidine (145 Da, Ligand)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
E. coli 70s ribosome (2 MDa, Complex from Escherichia coli)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
Spermine (202 Da, Ligand)
Mrna (9 kDa, RNA from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
E-site trna (589 Da, RNA from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
Water (18 Da, Ligand)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
16s rrna (499 kDa, RNA from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)

[Show more]

Sort by: Download

Showing 1 - 3 of 3. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [3]

Format:

Select the script type:

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

Preview first 10

Field: