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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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author:"Yokoyama T" AND xref_links:"alphafold" AND author_name:"H" AND xref_links:"scop2"

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EMD-9701

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Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii)

Release date: May 29, 2019
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6ip5
Q-score: 0.356

Yokoyama T, Machida K, Iwasaki W, Shigeta T, Nishimoto M, Takahashi M, Sakamoto A, Yonemochi M, Harada Y, Shigematsu H, Shirouzu M, Tadakuma H, Imataka H, Ito T

Mol Cell (2019) 74 pp. 1205-1214.e8 [ DOI: doi:10.1016/j.molcel.2019.04.022 Pubmed: 31080011 ]

Sample:

5.8s ribosomal rna (50 kDa, RNA from Homo sapiens)
40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
Nascent peptide (1 kDa, Protein from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
P-site trna (24 kDa, RNA from Homo sapiens)
40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
5s ribosomal rna (38 kDa, RNA from Homo sapiens)
60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
Mrna (1 kDa, RNA from Homo sapiens)
Human 80s ribosome (Complex from Homo sapiens)
40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
18s ribosomal rna (602 kDa, RNA from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
28s ribosomal rna (1 MDa, RNA from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l10-like (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)

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EMD-9702

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Cryo-EM structure of the CMV-stalled human 80S ribosome with HCV IRES (Structure iii)

Release date: May 29, 2019
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6ip6
Q-score: 0.184

Yokoyama T, Machida K, Iwasaki W, Shigeta T, Nishimoto M, Takahashi M, Sakamoto A, Yonemochi M, Harada Y, Shigematsu H, Shirouzu M, Tadakuma H, Imataka H, Ito T

Mol Cell (2019) 74 pp. 1205-1214.e8 [ DOI: doi:10.1016/j.molcel.2019.04.022 Pubmed: 31080011 ]

Sample:

5.8s ribosomal rna (50 kDa, RNA from Homo sapiens)
40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
Nascent peptide (1 kDa, Protein from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
P-site trna (24 kDa, RNA from Homo sapiens)
40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
5s ribosomal rna (38 kDa, RNA from Homo sapiens)
60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
Mrna (1 kDa, RNA from Homo sapiens)
Human 80s ribosome (Complex from Homo sapiens)
40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
18s ribosomal rna (602 kDa, RNA from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
28s ribosomal rna (1 MDa, RNA from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
Hcv-ires rna (93 kDa, RNA from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l10-like (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)

[Show more]

EMD-6747

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RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS

Release date: Aug. 16, 2017
Resolution: 3.83 Å
EM Method: Single-particle
Fitted PDBs: 5xon
Q-score: 0.336

Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI

Science (2017) 357 pp. 921-924 [ DOI: doi:10.1126/science.aan8552 Pubmed: 28775211 ]

Sample:

Dna (48-mer) (14 kDa, DNA from synthetic construct)
Rna (30-mer) (9 kDa, RNA from synthetic construct)
Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Magnesium ion (24 Da, Ligand)
Spt4/5 and tfiis (Complex)
Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Rna polymerase subunit abc14.5, common to rna polymerases i, ii, and iii (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Zinc ion (65 Da, Ligand)
Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Rna polymerase ii elongation complex bound with spt4/5 and tfiis (Complex from Komagataella pastoris)
Rna polymerase ii (Complex)
Protein that forms a complex with spt4p (68 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
General transcription elongation factor tfiis (21 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Rna polymerase subunit, found in rna polymerase complexes i, ii, and iii (7 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Dna (48-mer) (14 kDa, DNA from synthetic construct)
Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))

[Show more]

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Display: Statistics

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Select database:

EMDB [3]

Format:

Select the script type:

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

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Field: