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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:"uS7" AND xref_links:"chebi" AND xref_links:"uniprot" AND author_name:"D"

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EMD-44671

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The structure of human Pdcd4 bound to the 40S-eIF4A-eIF3-eIF1 complex

Release date: Sept. 4, 2024
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 9bln

Brito Querido J, Sokabe M, Diaz-Lopez I, Gordiyenko Y, Zuber P, Du Y, Albacete-Albacete L, Ramakrishnan V, Fraser CS

Nat Commun (2024) 15 pp. 6633-6633 [ Pubmed: 39117603 DOI: doi:10.1038/s41467-024-50672-8 ]

Sample:

Small ribosomal subunit protein es17 (15 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es26 (13 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us7 (22 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us19 (17 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es19 (16 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us17 (18 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 1 (12 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es8 (24 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit b (77 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es24 (15 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us2 (32 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es10 (18 kDa, Protein from Homo sapiens)
40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es25 (13 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es30 (6 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es7 (22 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es1 (30 kDa, Protein from Homo sapiens)
Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es12 (14 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
Potassium ion (39 Da, Ligand)
Small ribosomal subunit protein us8 (14 kDa, Protein from Homo sapiens)
Rrna (555 kDa, RNA from Homo sapiens)
Small ribosomal subunit protein us12 (15 kDa, Protein from Homo sapiens)
Pdcd4-40s-eif4a-eif3-eif1 complex (2 MDa, Complex from Homo sapiens)
Small ribosomal subunit protein us9 (16 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es21 (9 kDa, Protein from Homo sapiens)
Eukaryotic initiation factor 4a-i (44 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es4, x isoform (29 kDa, Protein from Homo sapiens)
Programmed cell death protein 4 (52 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
Spermidine (145 Da, Ligand)
Small ribosomal subunit protein es32 (3 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us15 (17 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us13 (17 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us14 (6 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us3 (26 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Acetic acid (60 Da, Ligand)
Small ribosomal subunit protein es6 (28 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Small ribosomal subunit protein us5 (31 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es27 (9 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us4 (22 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein es28 (7 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
Small ribosomal subunit protein us10 (13 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit i (36 kDa, Protein from Homo sapiens)
Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)

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EMD-17959

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Structure of bacterial ribosome determined by cryoEM at 100 keV

Release date: Nov. 29, 2023
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 8pva
Q-score: 0.287

McMullan G, Naydenova K, Mihaylov D, Yamashita K, Peet MJ, Wilson H, Dickerson JL, Chen S, Cannone G, Lee Y, Hutchings KA, Gittins O, Sobhy MA, Wells T, El-Gomati MM, Dalby J, Meffert M, Schulze-Briese C, Henderson R, Russo CJ

PNAS (2023) 120 pp. e2312905120-e2312905120 [ Pubmed: 38011573 DOI: doi:10.1073/pnas.2312905120 ]

Sample:

Small ribosomal subunit protein us7 (20 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein bs16 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us9 (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 l18 (12 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)
Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein bs6, fully modified isoform (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
A-site trna-val (24 kDa, RNA from Escherichia coli)
Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
Large ribosomal subunit protein bl31a (7 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)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us2 (26 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli)
Mrna (9 kDa, RNA from Escherichia coli)
Small ribosomal subunit protein bs20 (9 kDa, Protein from Escherichia coli)
Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli)
23s rrna (941 kDa, RNA from Escherichia coli)
Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
16s rrna (499 kDa, RNA from Escherichia coli)
Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli)
Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
E-site trna (589 Da, RNA from Escherichia coli)
Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
P-site trna-fmet (24 kDa, RNA from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
E. coli 70s ribosome (Complex from Escherichia coli)

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EMD-11232

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Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis

Release date: Oct. 7, 2020
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 6zj3
Q-score: 0.548

Matzov D, Taoka M, Nobe Y, Yamauchi Y, Halfon Y, Asis N, Zimermann E, Rozenberg H, Bashan A, Bhushan S, Isobe T, Gray MW, Yonath A, Shalev-Benami M

Nucleic Acids Res (2020) 48 pp. 11750-11761 [ DOI: doi:10.1093/nar/gkaa893 Pubmed: 33091122 ]

Sample:

Lsu rrna chain 4 (225 kDa, RNA from Euglena gracilis)
18s rrna (747 kDa, RNA from Euglena gracilis)
5s rrna (38 kDa, RNA from Euglena gracilis)
Ribosomal protein el32 (16 kDa, Protein from Euglena gracilis)
Ribosomal protein el37 (13 kDa, Protein from Euglena gracilis)
Water (18 Da, Ligand)
Ribosomal protein es19 (16 kDa, Protein from Euglena gracilis)
Ribosomal protein us2 (29 kDa, Protein from Euglena gracilis)
P-trna (24 kDa, RNA from Euglena gracilis)
Lsu rrna chain 10 (20 kDa, RNA from Euglena gracilis)
Lsu rrna chain 5 (170 kDa, RNA from Euglena gracilis)
Ribosomal protein es10 (17 kDa, Protein from Euglena gracilis)
Ribosomal protein us13 (17 kDa, Protein from Euglena gracilis)
Ribosomal protein el18 (21 kDa, Protein from Euglena gracilis)
Ribosomal protein es17 (16 kDa, Protein from Euglena gracilis)
Ribosomal protein es7 (22 kDa, Protein from Euglena gracilis)
Ribosomal protein el43 (12 kDa, Protein from Euglena gracilis)
Ribosomal protein el31 (17 kDa, Protein from Euglena gracilis)
Zinc ion (65 Da, Ligand)
Ribosomal protein el22 (18 kDa, Protein from Euglena gracilis)
Rack1 (34 kDa, Protein from Euglena gracilis)
Ribosomal protein ul4 (41 kDa, Protein from Euglena gracilis)
Ribosomal protein el39 (6 kDa, Protein from Euglena gracilis)
Lsu rrna chain 7 (240 kDa, RNA from Euglena gracilis)
Ribosomal protein es28 (8 kDa, Protein from Euglena gracilis)
Ribosomal protein el36 (12 kDa, Protein from Euglena gracilis)
Ribosomal protein us5 (27 kDa, Protein from Euglena gracilis)
Ribosomal protein ul15 (17 kDa, Protein from Euglena gracilis)
Ribosomal protein ul14 (14 kDa, Protein from Euglena gracilis)
Ribosomal protein es30 (7 kDa, Protein from Euglena gracilis)
Lsu rrna chain 11 (30 kDa, RNA from Euglena gracilis)
Ribosomal protein us17 (19 kDa, Protein from Euglena gracilis)
Ribosomal protein us19 (17 kDa, Protein from Euglena gracilis)
Ribosomal protein es31 (17 kDa, Protein from Euglena gracilis)
Ribosomal protein el41 (4 kDa, Protein from Euglena gracilis)
Ribosomal protein el19 (29 kDa, Protein from Euglena gracilis)
Ribosomal protein eseug1 (32 kDa, Protein from Euglena gracilis)
Lsu rrna chain 9 (52 kDa, RNA from Euglena gracilis)
Ribosomal protein ul24 (16 kDa, Protein from Euglena gracilis)
Lsu rrna chain 1 (42 kDa, RNA from Euglena gracilis)
60s ribosomal protein l7a (32 kDa, Protein from Euglena gracilis)
Ribosomal protein es24 (16 kDa, Protein from Euglena gracilis)
Ribosomal protein us12 (15 kDa, Protein from Euglena gracilis)
Ribosomal protein es1 (28 kDa, Protein from Euglena gracilis)
Euglena gracilis 80s ribosome (Complex from Euglena gracilis)
Ribosomal protein us9 (17 kDa, Protein from Euglena gracilis)
Ribosomal protein ul29 (14 kDa, Protein from Euglena gracilis)
Ribosomal protein us11 (16 kDa, Protein from Euglena gracilis)
Ribosomal protein elegr2 (8 kDa, Protein from Euglena gracilis)
Ribosomal protein us7 (21 kDa, Protein from Euglena gracilis)
60s ribosomal protein l10 (24 kDa, Protein from Euglena gracilis)
Ribosomal protein es27 (9 kDa, Protein from Euglena gracilis)
Ribosomal protein ul18 (29 kDa, Protein from Euglena gracilis)
Ribosomal protein el20 (21 kDa, Protein from Euglena gracilis)
Ribosomal protein us14 (6 kDa, Protein from Euglena gracilis)
Lsu rrna chain 8 (199 kDa, RNA from Euglena gracilis)
Ribosomal protein elegr3 (7 kDa, Protein from Euglena gracilis)
Ribosomal protein es12 (15 kDa, Protein from Euglena gracilis)
Ribosomal protein us4 (22 kDa, Protein from Euglena gracilis)
Ribosomal protein es21 (10 kDa, Protein from Euglena gracilis)
Ribosomal protein el40 (14 kDa, Protein from Euglena gracilis)
Ribosomal protein el27 (15 kDa, Protein from Euglena gracilis)
5.8s rrna (52 kDa, RNA from Euglena gracilis)
A-site trna (3 kDa, RNA from Euglena gracilis)
Ribosomal protein ul13 (24 kDa, Protein from Euglena gracilis)
A-trna (24 kDa, RNA from Euglena gracilis)
Ribosomal protein ul5 (21 kDa, Protein from Euglena gracilis)
Ribosomal protein es6 (31 kDa, Protein from Euglena gracilis)
Ribosomal protein el29 (13 kDa, Protein from Euglena gracilis)
Ribosomal protein ul3 (46 kDa, Protein from Euglena gracilis)
Ribosomal protein es8 (35 kDa, Protein from Euglena gracilis)
Ribosomal protein ul22 (18 kDa, Protein from Euglena gracilis)
Ribosomal protein es26 (13 kDa, Protein from Euglena gracilis)
Ribosomal protein ul2 (28 kDa, Protein from Euglena gracilis)
Ribosomal protein el33 (13 kDa, Protein from Euglena gracilis)
Ribosomal protein ul30 (28 kDa, Protein from Euglena gracilis)
Lsu rrna chain 6 (75 kDa, RNA from Euglena gracilis)
Ribosomal protein el21 (18 kDa, Protein from Euglena gracilis)
Ribosomal protein el34 (14 kDa, Protein from Euglena gracilis)
Ribosomal protein el30 (12 kDa, Protein from Euglena gracilis)
Lsu rrna chain 2 (113 kDa, RNA from Euglena gracilis)
Ribosomal protein us8 (14 kDa, Protein from Euglena gracilis)
Ribosomal protein es4 (31 kDa, Protein from Euglena gracilis)
Ribosomal protein el24 (17 kDa, Protein from Euglena gracilis)
Ribosomal protein us10 (13 kDa, Protein from Euglena gracilis)
Ribosomal protein us3 (24 kDa, Protein from Euglena gracilis)
Ribosomal protein ul23 (18 kDa, Protein from Euglena gracilis)
Lsu rrna chain 3 (37 kDa, RNA from Euglena gracilis)
Ribosomal protein el42 (10 kDa, Protein from Euglena gracilis)
Lsu rrna chain 13 (27 kDa, RNA from Euglena gracilis)
Ribosomal protein el14 (25 kDa, Protein from Euglena gracilis)
Ribosomal protein es25 (13 kDa, Protein from Euglena gracilis)
Ribosomal protein elegr1 (7 kDa, Protein from Euglena gracilis)
Ribosomal protein ul6 (22 kDa, Protein from Euglena gracilis)
Ribosomal protein el38 (9 kDa, Protein from Euglena gracilis)
Ribosomal protein us15 (17 kDa, Protein from Euglena gracilis)
Ribosomal protein el6 (22 kDa, Protein from Euglena gracilis)
Lsu rrna chain 12 (18 kDa, RNA from Euglena gracilis)
Ribosomal protein el15 (24 kDa, Protein from Euglena gracilis)
E-trna (24 kDa, RNA from Euglena gracilis)
Ribosomal protein el13 (25 kDa, Protein from Euglena gracilis)

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EMD-8149

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Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-INconformation

Release date: Dec. 7, 2016
Resolution: 5.34 Å
EM Method: Single-particle
Fitted PDBs: 5jbh
Q-score: 0.117

Coureux PD, Lazennec-Schurdevin C, Monestier A, Larquet E, Cladiere L, Klaholz BP, Schmitt E, Mechulam Y

Nat Commun (2016) 7 pp. 13366-13366 [ DOI: doi:10.1038/ncomms13366 Pubmed: 27819266 ]

Sample:

30s ribosomal protein us15 (18 kDa, Protein from Pyrococcus abyssi GE5)
Aif2-beta (15 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us7 (24 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us2 (23 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us5 (26 kDa, Protein from Pyrococcus abyssi GE5)
Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
30s ribosomal protein es28 (8 kDa, Protein from Pyrococcus abyssi GE5)
30s archaeal translation initiation complex (Complex from Escherichia coli)
30s ribosomal protein us8 (14 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein sx (4 kDa, Protein from Pyrococcus abyssi GE5)
Aif1a (13 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein es8 (14 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us14 (6 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein es24 (11 kDa, Protein from Pyrococcus abyssi GE5)
30s archaeal translation initiation complex (Complex from Pyrococcus)
Mrna (8 kDa, RNA from Pyrococcus)
30s ribosomal protein us3 (23 kDa, Protein from Pyrococcus abyssi GE5)
Methionine (149 Da, Ligand)
30s ribosomal protein us12 (16 kDa, Protein from Pyrococcus abyssi GE5)
50s ribosomal protein ul30 (13 kDa, Protein from Pyrococcus abyssi GE5)
Aif2-alpha (30 kDa, Protein from Pyrococcus abyssi GE5)
30s archaeal translation initiation complex (982 kDa, Complex)
Aif1 (11 kDa, Protein from Pyrococcus abyssi GE5)
16s ribosomal rna (492 kDa, RNA from Pyrococcus abyssi GE5)
Initiator met-trna fmet from e. coli (a1u72 variant) (24 kDa, RNA from Escherichia coli)
30s ribosomal protein es27 (5 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein el41 (3 kDa, Protein from Pyrococcus abyssi GE5)
Magnesium ion (24 Da, Ligand)
30s ribosomal protein us13 (16 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us9 (15 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us4 (21 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us11 (14 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us19 (15 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us3 (22 kDa, Protein from Pyrococcus abyssi GE5)
Zinc ion (65 Da, Ligand)
30s ribosomal protein es17 (7 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us17 (13 kDa, Protein from Pyrococcus abyssi GE5)
Aif2-gamma (45 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein es27 (6 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein us10 (11 kDa, Protein from Pyrococcus abyssi GE5)
30s archaeal translation initiation complex (Complex from Pyrococcus abyssi GE5)
30s ribosomal protein es4 (28 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein es19 (17 kDa, Protein from Pyrococcus abyssi GE5)
30s ribosomal protein es6 (14 kDa, Protein from Pyrococcus abyssi GE5)

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Display: Statistics

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Select database:

EMDB [4]

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