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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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primary_citation_author:"Fernandez IS" AND release_date:[2020-01-01T00:00:00Z TO 2020-12-31T23:59:59Z]

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EMD-21859

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CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP

Release date: Sept. 23, 2020
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6woo
Q-score: 0.487

Wang J, Wang J, Puglisi J, Fernandez IS

To Be Published

Sample:

Us14 (6 kDa, Protein from Saccharomyces cerevisiae)
Es8 (22 kDa, Protein from Saccharomyces cerevisiae)
Us11 (13 kDa, Protein from Saccharomyces cerevisiae)
El31 (12 kDa, Protein from Saccharomyces cerevisiae)
Us12 (15 kDa, Protein from Saccharomyces cerevisiae)
Ul5 (19 kDa, Protein from Saccharomyces cerevisiae)
Ul14 (14 kDa, Protein from Saccharomyces cerevisiae)
El36 (10 kDa, Protein from Saccharomyces cerevisiae)
Es4 (29 kDa, Protein from Saccharomyces cerevisiae)
El32 (14 kDa, Protein from Saccharomyces cerevisiae)
El40 (5 kDa, Protein from Saccharomyces cerevisiae)
El24 (7 kDa, Protein from Saccharomyces cerevisiae)
Us10 (12 kDa, Protein from Saccharomyces cerevisiae)
Us7 (22 kDa, Protein from Saccharomyces cerevisiae)
El14 (14 kDa, Protein from Saccharomyces cerevisiae)
El18 (20 kDa, Protein from Saccharomyces cerevisiae)
El37 (9 kDa, Protein from Saccharomyces cerevisiae)
El41 (3 kDa, Protein from Saccharomyces cerevisiae)
Guanosine-5'-diphosphate (443 Da, Ligand)
El42 (11 kDa, Protein from Saccharomyces cerevisiae)
Es26 (11 kDa, Protein from Saccharomyces cerevisiae)
Us5 (23 kDa, Protein from Saccharomyces cerevisiae)
El13 (22 kDa, Protein from Saccharomyces cerevisiae)
Es19 (15 kDa, Protein from Saccharomyces cerevisiae)
Ul3 (43 kDa, Protein from Saccharomyces cerevisiae)
5.8s ribosomal rrna (50 kDa, RNA from Saccharomyces cerevisiae)
Ul6 (21 kDa, Protein from Saccharomyces cerevisiae)
Es25 (8 kDa, Protein from Saccharomyces cerevisiae)
Es24 (15 kDa, Protein from Saccharomyces cerevisiae)
Es28 (7 kDa, Protein from Saccharomyces cerevisiae)
Es1 (24 kDa, Protein from Saccharomyces cerevisiae)
Es10 (11 kDa, Protein from Saccharomyces cerevisiae)
El29 (6 kDa, Protein from Saccharomyces cerevisiae)
Es31 (6 kDa, Protein from Saccharomyces cerevisiae)
Es12 (13 kDa, Protein from Saccharomyces cerevisiae)
Ul10 (21 kDa, Protein from Saccharomyces cerevisiae)
Ul13 (22 kDa, Protein from Saccharomyces cerevisiae)
Us2 (22 kDa, Protein from Saccharomyces cerevisiae)
Met-trna-imet (24 kDa, RNA from Saccharomyces cerevisiae)
Methionine (149 Da, Ligand)
Us8 (14 kDa, Protein from Saccharomyces cerevisiae)
El34 (13 kDa, Protein from Saccharomyces cerevisiae)
5s ribosomal rna (38 kDa, RNA from Saccharomyces cerevisiae)
El22 (11 kDa, Protein from Saccharomyces cerevisiae)
Ul2 (26 kDa, Protein from Saccharomyces cerevisiae)
Ul29 (13 kDa, Protein from Saccharomyces cerevisiae)
El27 (15 kDa, Protein from Saccharomyces cerevisiae)
El33 (11 kDa, Protein from Saccharomyces cerevisiae)
Us19 (11 kDa, Protein from Saccharomyces cerevisiae)
L10 (12 kDa, Protein from Saccharomyces cerevisiae)
Ul15 (16 kDa, Protein from Saccharomyces cerevisiae)
El43 (9 kDa, Protein from Saccharomyces cerevisiae)
Ul22 (20 kDa, Protein from Saccharomyces cerevisiae)
El39 (6 kDa, Protein from Saccharomyces cerevisiae)
Es21 (9 kDa, Protein from Saccharomyces cerevisiae)
Us4 (20 kDa, Protein from Saccharomyces cerevisiae)
Ul24 (14 kDa, Protein from Saccharomyces cerevisiae)
Es17 (14 kDa, Protein from Saccharomyces cerevisiae)
El8 (25 kDa, Protein from Saccharomyces cerevisiae)
Ul16 (24 kDa, Protein from Saccharomyces cerevisiae)
Mrna (1 kDa, RNA from Saccharomyces cerevisiae)
El21 (18 kDa, Protein from Saccharomyces cerevisiae)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae)
Us3 (24 kDa, Protein from Saccharomyces cerevisiae)
El15 (24 kDa, Protein from Saccharomyces cerevisiae)
Zinc ion (65 Da, Ligand)
Es27 (8 kDa, Protein from Saccharomyces cerevisiae)
Us19 (15 kDa, Protein from Saccharomyces cerevisiae)
Ul1 (24 kDa, Protein from Saccharomyces cerevisiae)
Ul4 (38 kDa, Protein from Saccharomyces cerevisiae)
El20 (20 kDa, Protein from Saccharomyces cerevisiae)
Rack1 (34 kDa, Protein from Saccharomyces cerevisiae)
Es30 (6 kDa, Protein from Saccharomyces cerevisiae)
El19 (21 kDa, Protein from Saccharomyces cerevisiae)
El30 (10 kDa, Protein from Saccharomyces cerevisiae)
N-carboxy-l-threonine (163 Da, Ligand)
Us15 (16 kDa, Protein from Saccharomyces cerevisiae)
Ul18 (33 kDa, Protein from Saccharomyces cerevisiae)
El6 (19 kDa, Protein from Saccharomyces cerevisiae)
Es7 (21 kDa, Protein from Saccharomyces cerevisiae)
Eif5b (67 kDa, Protein from Saccharomyces cerevisiae)
Ul30 (25 kDa, Protein from Saccharomyces cerevisiae)
18s ribosomal rna (578 kDa, RNA from Saccharomyces cerevisiae)
El38 (8 kDa, Protein from Saccharomyces cerevisiae)
Us13 (15 kDa, Protein from Saccharomyces cerevisiae)
80s ribosome with eif5b, met-trnaimet, mrna, and gdp (Complex from Saccharomyces cerevisiae)
Us17 (16 kDa, Protein from Saccharomyces cerevisiae)
Es6 (25 kDa, Protein from Saccharomyces cerevisiae)
Ul23 (13 kDa, Protein from Saccharomyces cerevisiae)

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EMD-21531

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Head masked 3D refined density of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit used to build the 5-UTR IRES model

Release date: April 29, 2020
Resolution: 2.79 Å
EM Method: Single-particle

Neupane R, Pisareva VP, Rodriguez CF, Pisarev AV, Fernandez IS

eLife (2020) 9 [ Pubmed: 32286223 DOI: doi:10.7554/eLife.54575 ]

Sample:

Cricket paralysis virus 5-utr ires (crpv 5-utr-ires) bound to the small ribosomal subunit from a head masked 3d refinement (Complex from Oryctolagus cuniculus)

EMD-21529

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Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1)

Release date: April 22, 2020
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 6w2s
Q-score: 0.415

Neupane R, Pisareva VP, Rodriguez CF, Pisarev AV, Fernandez IS

eLife (2020) 9 [ DOI: doi:10.7554/eLife.54575 Pubmed: 32286223 ]

Sample:

Es28 (7 kDa, Protein from Oryctolagus cuniculus)
Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
Es12 (14 kDa, Protein from Oryctolagus cuniculus)
Us9 (19 kDa, Protein from Oryctolagus cuniculus)
Es17 (15 kDa, Protein from Oryctolagus cuniculus)
Es10 (17 kDa, Protein from Oryctolagus cuniculus)
Es31 (18 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit h (41 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Oryctolagus cuniculus)
Es8 (24 kDa, Protein from Oryctolagus cuniculus)
Es7 (22 kDa, Protein from Oryctolagus cuniculus)
Es21 (9 kDa, Protein from Oryctolagus cuniculus)
Es4 (29 kDa, Protein from Oryctolagus cuniculus)
Es6 (28 kDa, Protein from Oryctolagus cuniculus)
Us10 (13 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit a (164 kDa, Protein from Oryctolagus cuniculus)
Es1 (30 kDa, Protein from Oryctolagus cuniculus)
Us4 (22 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit l (71 kDa, Protein from Oryctolagus cuniculus)
18s rrna (547 kDa, RNA from Oryctolagus cuniculus)
Es24 (15 kDa, Protein from Oryctolagus cuniculus)
Es30 (14 kDa, Protein from Oryctolagus cuniculus)
Us12 (15 kDa, Protein from Oryctolagus cuniculus)
Us7 (22 kDa, Protein from Oryctolagus cuniculus)
Es25 (13 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Oryctolagus cuniculus)
Zinc ion (65 Da, Ligand)
Us5 (27 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Oryctolagus cuniculus)
Crpv 5'-utr ires (121 kDa, RNA from Cricket paralysis virus)
Us3 (31 kDa, Protein from Oryctolagus cuniculus)
Us13 (17 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Oryctolagus cuniculus)
Us8 (14 kDa, Protein from Oryctolagus cuniculus)
Us19 (17 kDa, Protein from Oryctolagus cuniculus)
Us2 (33 kDa, Protein from Oryctolagus cuniculus)
Es27 (9 kDa, Protein from Oryctolagus cuniculus)
Magnesium ion (24 Da, Ligand)
Us17 (18 kDa, Protein from Oryctolagus cuniculus)
Structure of the cricket paralysis virus 5-utr ires (crpv 5-utr-ires) bound to the small ribosomal subunit in the open state (class 1) (Complex from Oryctolagus cuniculus)
Us15 (17 kDa, Protein from Oryctolagus cuniculus)
Es26 (13 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit e (54 kDa, Protein from Oryctolagus cuniculus)
Es19 (16 kDa, Protein from Oryctolagus cuniculus)
Es29 (6 kDa, Protein from Oryctolagus cuniculus)
Us11 (16 kDa, Protein from Oryctolagus cuniculus)

[Show more]

EMD-21530

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Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)

Release date: April 22, 2020
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 6w2t
Q-score: 0.42

Neupane R, Pisareva VP, Rodriguez CF, Pisarev AV, Fernandez IS

eLife (2020) 9 [ Pubmed: 32286223 DOI: doi:10.7554/eLife.54575 ]

Sample:

Es26 (13 kDa, Protein from Oryctolagus cuniculus)
Us10 (13 kDa, Protein from Oryctolagus cuniculus)
Es29 (6 kDa, Protein from Oryctolagus cuniculus)
Us8 (14 kDa, Protein from Oryctolagus cuniculus)
Es6 (28 kDa, Protein from Oryctolagus cuniculus)
Es28 (7 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Oryctolagus cuniculus)
Es4 (29 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit e (54 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit h (41 kDa, Protein from Oryctolagus cuniculus)
Magnesium ion (24 Da, Ligand)
Us2 (33 kDa, Protein from Oryctolagus cuniculus)
Es31 (18 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit l (71 kDa, Protein from Oryctolagus cuniculus)
Us9 (19 kDa, Protein from Oryctolagus cuniculus)
18s rrna (547 kDa, RNA from Oryctolagus cuniculus)
Es1 (30 kDa, Protein from Oryctolagus cuniculus)
Es21 (9 kDa, Protein from Oryctolagus cuniculus)
Us19 (17 kDa, Protein from Oryctolagus cuniculus)
Us13 (17 kDa, Protein from Oryctolagus cuniculus)
Es19 (16 kDa, Protein from Oryctolagus cuniculus)
Us15 (17 kDa, Protein from Oryctolagus cuniculus)
Es17 (15 kDa, Protein from Oryctolagus cuniculus)
Us5 (27 kDa, Protein from Oryctolagus cuniculus)
Es7 (22 kDa, Protein from Oryctolagus cuniculus)
Us4 (22 kDa, Protein from Oryctolagus cuniculus)
Us12 (15 kDa, Protein from Oryctolagus cuniculus)
Es30 (14 kDa, Protein from Oryctolagus cuniculus)
Es24 (15 kDa, Protein from Oryctolagus cuniculus)
Zinc ion (65 Da, Ligand)
Eukaryotic translation initiation factor 3 subunit a (164 kDa, Protein from Oryctolagus cuniculus)
Us11 (16 kDa, Protein from Oryctolagus cuniculus)
Es8 (24 kDa, Protein from Oryctolagus cuniculus)
Es27 (9 kDa, Protein from Oryctolagus cuniculus)
Us7 (22 kDa, Protein from Oryctolagus cuniculus)
Us17 (18 kDa, Protein from Oryctolagus cuniculus)
Crpv 5'-utr ires (121 kDa, RNA from Cricket paralysis virus)
Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Oryctolagus cuniculus)
Es25 (13 kDa, Protein from Oryctolagus cuniculus)
Es12 (14 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Oryctolagus cuniculus)
Structure of the cricket paralysis virus 5-utr ires (crpv 5-utr-ires) bound to the small ribosomal subunit in the closed state (class 2) (Complex from Oryctolagus cuniculus)
Es10 (17 kDa, Protein from Oryctolagus cuniculus)
Us3 (31 kDa, Protein from Oryctolagus cuniculus)
Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Oryctolagus cuniculus)
Rack1 (35 kDa, Protein from Oryctolagus cuniculus)

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EMD-20952

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K.lactis 80S ribosome with p/PE tRNA and eIF5B

Release date: Jan. 15, 2020
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6uz7
Q-score: 0.39

Huang BY, Fernandez IS

PNAS (2020) 117 pp. 1429-1437 [ DOI: doi:10.1073/pnas.1916436117 Pubmed: 31900355 ]

Sample:

Klla0e23651p (18 kDa, Protein from Kluyveromyces lactis)
Klla0a10483p (17 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s22 (14 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l13 (22 kDa, Protein from Kluyveromyces lactis)
Klla0d06941p (33 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l41 (3 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s0 (28 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s24 (15 kDa, Protein from Kluyveromyces lactis)
Kluyveromyces lactis 80s ribosome in complex with eif5b (Complex from Kluyveromyces lactis)
Ribosomal protein l37 (9 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s7 (21 kDa, Protein from Kluyveromyces lactis)
Rps23 (16 kDa, Protein from Kluyveromyces lactis)
Klla0e06843p (14 kDa, Protein from Kluyveromyces lactis)
Klla0e05941p (9 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s6 (26 kDa, Protein from Kluyveromyces lactis)
Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
Klla0e23673p (21 kDa, Protein from Kluyveromyces lactis)
Gdpcp (12 kDa, Protein from Kluyveromyces lactis)
60s acidic ribosomal protein p0 (33 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s25 (12 kDa, Protein from Kluyveromyces lactis)
Ubiquitin-40s ribosomal protein s27a (17 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l29 (7 kDa, Protein from Kluyveromyces lactis)
Klla0d10659p (25 kDa, Protein from Kluyveromyces lactis)
Ribosomal protein (24 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l36 (11 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l20 (20 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s21 (9 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s14 (14 kDa, Protein from Kluyveromyces lactis)
Klla0b08173p (12 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s8 (22 kDa, Protein from Kluyveromyces lactis)
Klla0f23265p (108 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l24 (17 kDa, Protein from Kluyveromyces lactis)
Rna (76-mer) (24 kDa, RNA from Saccharomyces cerevisiae)
Klla0a07194p (15 kDa, Protein from Kluyveromyces lactis)
Klla0d05181p (13 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l3 (43 kDa, Protein from Kluyveromyces lactis)
Klla0a07227p (20 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s26 (13 kDa, Protein from Kluyveromyces lactis)
Klla0b07139p (39 kDa, Protein from Kluyveromyces lactis)
Klla0d16027p (27 kDa, Protein from Kluyveromyces lactis)
Klla0f09812p (27 kDa, Protein from Kluyveromyces lactis)
Klla0c08371p (14 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l39 (6 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l30 (11 kDa, Protein from Kluyveromyces lactis)
Klla0f04499p (21 kDa, Protein from Kluyveromyces lactis)
Klla0d03410p (27 kDa, Protein from Kluyveromyces lactis)
25s ribosomal rna (1 MDa, RNA from Kluyveromyces lactis)
Klla0f18040p (16 kDa, Protein from Kluyveromyces lactis)
60s ribosomal protein l44 (12 kDa, Protein from Kluyveromyces lactis)
Ribosomal protein l15 (24 kDa, Protein from Kluyveromyces lactis)
Klla0d08305p (26 kDa, Protein from Kluyveromyces lactis)
Klla0e00573p (28 kDa, Protein from Kluyveromyces lactis)
Klla0f25542p (13 kDa, Protein from Kluyveromyces lactis)
Klla0e12277p (35 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s28 (7 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s30 (7 kDa, Protein from Kluyveromyces lactis)
Klla0f07843p (15 kDa, Protein from Kluyveromyces lactis)
Klla0e03455p (15 kDa, Protein from Kluyveromyces lactis)
18s ribosomal rna (579 kDa, RNA from Kluyveromyces lactis)
60s ribosomal protein l25 (15 kDa, Protein from Kluyveromyces lactis)
Klla0c18216p (8 kDa, Protein from Kluyveromyces lactis)
Klla0e12453p (21 kDa, Protein from Kluyveromyces lactis)
Klla0f04675p (22 kDa, Protein from Kluyveromyces lactis)
Klla0e06997p (14 kDa, Protein from Kluyveromyces lactis)
Klla0b01562p (17 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s29 (6 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s27 (8 kDa, Protein from Kluyveromyces lactis)
Klla0d07405p (12 kDa, Protein from Kluyveromyces lactis)
Klla0b13409p (15 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s16 (15 kDa, Protein from Kluyveromyces lactis)
Klla0b01474p (15 kDa, Protein from Kluyveromyces lactis)
Rna (121-mer) (38 kDa, RNA from Kluyveromyces lactis)
40s ribosomal protein s1 (28 kDa, Protein from Kluyveromyces lactis)
Zinc ion (65 Da, Ligand)
Klla0a06336p (20 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s12 (14 kDa, Protein from Kluyveromyces lactis)
Klla0f05247p (14 kDa, Protein from Kluyveromyces lactis)
Klla0d05643p (25 kDa, Protein from Kluyveromyces lactis)
Klla0b05742p (14 kDa, Protein from Kluyveromyces lactis)
5.8s ribosomal rna (910 kDa, RNA from Kluyveromyces lactis)
Klla0b02937p (13 kDa, Protein from Kluyveromyces lactis)
Klla0f08261p (19 kDa, Protein from Kluyveromyces lactis)
Rpl28 (16 kDa, Protein from Kluyveromyces lactis)
40s ribosomal protein s4 (29 kDa, Protein from Kluyveromyces lactis)
Ubiquitin fusion protein (14 kDa, Protein from Kluyveromyces lactis)
Klla0b04686p (20 kDa, Protein from Kluyveromyces lactis)

[Show more]

Sort by: Download

Showing 1 - 5 of 5. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [5]

Format:

Select the script type:

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

Preview first 10

Field: