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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 xref_links:"interpro" AND xref_links:"empiar"

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EMD-15488

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Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome

Release date: March 8, 2023
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8akn
Q-score: 0.647

Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN

Nat Chem Biol (2023) 19 pp. 1072-1081 [ DOI: doi:10.1038/s41589-023-01293-7 Pubmed: 36997646 ]

Sample:

30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BW25113)
Phenylalanine-trna (24 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli BW25113)
Mrna (2 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli BW25113)
Peptide chain release factor rf1 (40 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
2-acetamido-2-deoxy-alpha-d-galactopyranose (221 Da, Ligand)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BW25113)
Drosocin1 (2 kDa, Protein from Drosophila melanogaster)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BW25113)
Spermine (202 Da, Ligand)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BW25113)
Isoleucine-trna (24 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli BW25113)
Zinc ion (65 Da, Ligand)
5s ribosomal rna (38 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli BW25113)
23s ribosomal rna (941 kDa, RNA from Escherichia coli BW25113)
Water (18 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BW25113)
Magnesium ion (24 Da, Ligand)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BW25113)
Cryo-em structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome (2 MDa, Complex from Escherichia coli BW25113)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli BW25113)
16s ribosomal rna (497 kDa, RNA from Escherichia coli BW25113)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)

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EMD-15523

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Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome

Release date: March 8, 2023
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8am9
Q-score: 0.594

Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN

Nat Chem Biol (2023) 19 pp. 1072-1081 [ DOI: doi:10.1038/s41589-023-01293-7 Pubmed: 36997646 ]

Sample:

23s ribosomal rna (941 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli BW25113)
16s ribosomal rna (497 kDa, RNA from Escherichia coli BW25113)
30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli BW25113)
Mrna (3 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli BW25113)
Cryo-em structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome (2 MDa, Complex from Escherichia coli K-12)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BW25113)
Initiator trna (24 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BW25113)
Magnesium ion (24 Da, Ligand)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BW25113)
5s ribosomal rna (38 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BW25113)
Spermine (202 Da, Ligand)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BW25113)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli BW25113)
Leucine trna (27 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BW25113)
2-acetamido-2-deoxy-alpha-d-galactopyranose (221 Da, Ligand)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli BW25113)
Drosocin1 (2 kDa, Protein from Drosophila melanogaster)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BW25113)
Water (18 Da, Ligand)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli BW25113)

[Show more]

EMD-15533

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Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit

Release date: March 8, 2023
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 8ana
Q-score: 0.695

Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN

Nat Chem Biol (2023) 19 pp. 1072-1081 [ DOI: doi:10.1038/s41589-023-01293-7 Pubmed: 36997646 ]

Sample:

50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BW25113)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BW25113)
5s ribosomal rna (38 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BW25113)
Spermine (202 Da, Ligand)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BW25113)
Cryo-em structure of the proline-rich antimicrobial peptide drosocin bound to the 50s ribosomal subunit (1 MDa, Complex from Escherichia coli K-12)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BW25113)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BW25113)
2-acetamido-2-deoxy-alpha-d-galactopyranose (221 Da, Ligand)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli BW25113)
Drosocin1 (2 kDa, Protein from Drosophila melanogaster)
23s ribosomal rna (941 kDa, RNA from Escherichia coli BW25113)
Water (18 Da, Ligand)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli BW25113)

[Show more]

EMD-32068

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Cryo-EM structure of the human ATP13A2 (SPM-bound E2P state)

Release date: Dec. 29, 2021
Resolution: 3.92 Å
EM Method: Single-particle
Fitted PDBs: 7vpk
Q-score: 0.369

Tomita A, Daiho T, Kusakizako T, Yamashita K, Ogasawara S, Murata T, Nishizawa T, Nureki O

Mol Cell (2021) 81 pp. 4799-4809.e5 [ Pubmed: 34798056 DOI: doi:10.1016/j.molcel.2021.11.001 ]

Sample:

Spermine (202 Da, Ligand)
Beryllium trifluoride ion (66 Da, Ligand)
Atp13a2 (Complex from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Polyamine-transporting atpase 13a2 (129 kDa, Protein from Homo sapiens)

[Show more]

EMD-32069

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Cryo-EM structure of the human ATP13A2 (SPM-bound E2Pi state)

Release date: Dec. 29, 2021
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 7vpl
Q-score: 0.349

Tomita A, Daiho T, Kusakizako T, Yamashita K, Ogasawara S, Murata T, Nishizawa T, Nureki O

Mol Cell (2021) 81 pp. 4799-4809.e5 [ Pubmed: 34798056 DOI: doi:10.1016/j.molcel.2021.11.001 ]

Sample:

Tetrafluoroaluminate ion (102 Da, Ligand)
Magnesium ion (24 Da, Ligand)
Spermine (202 Da, Ligand)
Atp13a2 (Complex from Homo sapiens)
Polyamine-transporting atpase 13a2 (129 kDa, Protein from Homo sapiens)

[Show more]

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]

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Showing 1 - 6 of 6. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [6]

Format:

Select the script type:

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

Preview first 10

Field: