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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:"Hong S" AND xref_links:"pfam" AND resolution:[3 TO 4} AND author_name:"Y"

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EMD-30985

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Cryo-EM structure of the yeast mitochondrial SAM-Tom40 complex at 3.0 angstrom

Release date: Sept. 1, 2021
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 7e4h
Q-score: 0.445

Wang Q, Guan Z, Qi L, Zhuang J, Wang C, Hong S, Yan L, Wu Y, Cao X, Cao J, Yan J, Zou T, Liu Z, Zhang D, Yan C, Yin P

Science (2021) 373 pp. 1377-1381 [ Pubmed: 34446444 DOI: doi:10.1126/science.abh0704 ]

Sample:

Sorting assembly machinery subunits (Complex from Saccharomyces cerevisiae S288c)
Mitochondrial import receptor subunit tom40 (46 kDa, Protein from Saccharomyces cerevisiae S288c)
Sam-tom40 complex (Complex from Saccharomyces cerevisiae S288c)
Sorting assembly machinery 50 kda subunit (54 kDa, Protein from Saccharomyces cerevisiae S288c)
Sorting assembly machinery 35 kda subunit (37 kDa, Protein from Saccharomyces cerevisiae S288c)
Sorting assembly machinery 37 kda subunit (40 kDa, Protein from Saccharomyces cerevisiae S288c)
Mitochondrial import receptor subunit tom40 (Complex)

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EMD-30986

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Cryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex at 3.0 angstrom

Release date: Sept. 1, 2021
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 7e4i
Q-score: 0.485

Wang Q, Guan Z, Qi L, Zhuang J, Wang C, Hong S, Yan L, Wu Y, Cao X, Cao J, Yan J, Zou T, Liu Z, Zhang D, Yan C, Yin P

Science (2021) 373 pp. 1377-1381 [ Pubmed: 34446444 DOI: doi:10.1126/science.abh0704 ]

Sample:

Sorting assembly machinery subunits (Complex from Saccharomyces cerevisiae S288c)
Mitochondrial import receptor subunits (Complex)
Sorting assembly machinery 50 kda subunit (54 kDa, Protein from Saccharomyces cerevisiae S288c)
Sorting assembly machinery 35 kda subunit (37 kDa, Protein from Saccharomyces cerevisiae S288c)
Sorting assembly machinery 37 kda subunit (40 kDa, Protein from Saccharomyces cerevisiae S288c)
Mitochondrial import receptor subunit tom6 (6 kDa, Protein from Saccharomyces cerevisiae S288c)
Mitochondrial import receptor subunit tom5 (6 kDa, Protein from Saccharomyces cerevisiae S288c)
Mitochondrial import receptor subunit tom40 (43 kDa, Protein from Saccharomyces cerevisiae S288c)
Sam-tom40/tom5/tom6 complex (Complex from Saccharomyces cerevisiae S288c)

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EMD-9958

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Cryo-EM structure of the human mitochondrial translocase TIM22 complex at 3.7 angstrom.

Release date: Oct. 14, 2020
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7cgp
Q-score: 0.394

Qi L, Wang Q, Guan Z, Wu Y, Shen C, Hong S, Cao J, Zhang X, Yan C, Yin P

Cell Res (2020) [ Pubmed: 32901109 DOI: doi:10.1038/s41422-020-00400-w ]

Sample:

Mitochondrial import inner membrane translocase subunit tim22 (20 kDa, Protein from Homo sapiens)
Mitochondrial import inner membrane translocase subunit tim9 (10 kDa, Protein from Homo sapiens)
Mitochondrial import inner membrane translocase subunit tim10 (10 kDa, Protein from Homo sapiens)
Acylglycerol kinase, mitochondrial (47 kDa, Protein from Homo sapiens)
Mitochondrial import inner membrane translocase subunit tim29 (29 kDa, Protein from Homo sapiens)
Tim22 translocase (220 MDa, Complex from Homo sapiens)
Mitochondrial import inner membrane translocase subunit tim10 b (11 kDa, Protein from Homo sapiens)
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (749 Da, Ligand)

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EMD-7286

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Cryo-EM density map of Alternative Complex III from Flavobacterium johnsoniae (Wild Type)

Release date: May 9, 2018
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6btm
Q-score: 0.482

Sun C, Benlekbir S, Venkatakrishnan P, Wang Y, Hong S, Hosler J, Tajkhorshid E, Rubinstein JL, Gennis RB

Nature (2018) 557 pp. 123-126 [ DOI: doi:10.1038/s41586-018-0061-y Pubmed: 29695868 ]

Sample:

Fe3-s4 cluster (295 Da, Ligand)
Alternative complex iii subunit f (52 kDa, Protein from Flavobacterium johnsoniae UW101)
Decanoic acid (172 Da, Ligand)
Alternative complex iii subunit e (18 kDa, Protein from Flavobacterium johnsoniae UW101)
(2s)-3-hydroxypropane-1,2-diyl ditetradecanoate (512 Da, Ligand)
Alternative complex iii subunit d (19 kDa, Protein from Flavobacterium johnsoniae UW101)
Alternative complex iii subunit a (48 kDa, Protein from Flavobacterium johnsoniae UW101)
Iron/sulfur cluster (351 Da, Ligand)
Aciii-cyt aa3 supercomplex (Complex from Flavobacterium johnsoniae UW101)
Heme c (618 Da, Ligand)
Alternative complex iii subunit c (53 kDa, Protein from Flavobacterium johnsoniae UW101)
Alternative complex iii subunit b (102 kDa, Protein from Flavobacterium johnsoniae UW101)

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EMD-8596

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70S ribosome complex with dnaX mRNA stemloop and E-site tRNA ("in" conformation)

Release date: March 7, 2018
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 5uq7
Q-score: 0.397

Zhang Y, Hong S, Ruangprasert A, Skiniotis G, Dunham CM

Structure (2018) 26 pp. 437-445.e3 [ Pubmed: 29456023 DOI: doi:10.1016/j.str.2018.01.013 ]

Sample:

5s rrna (38 kDa, RNA from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s2 (26 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s13 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l15 (16 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l22 (12 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l36 (4 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l4 (22 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s6 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l19 (15 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l30 (6 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l5 (20 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s15 (10 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
23s rrna (948 kDa, RNA from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s17 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l33 (6 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
P-site trna fmet (24 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l20 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l28 (10 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s12 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s16 (9 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l14 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l2 (30 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l34 (5 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l27 (8 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l6 (18 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein thx (2 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l18 (12 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l21 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l17 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Messenger rna (17 kDa, RNA from synthetic construct)
50s ribosomal protein l13 (15 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s14 type z (7 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
E-site trna phe (24 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l24 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s18 (7 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l35 (7 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s3 (22 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l32 (6 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l1 (24 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s20 (10 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s4 (24 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l3 (22 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l16 (15 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s9 (14 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Zinc ion (65 Da, Ligand)
50s ribosomal protein l29 (8 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l25 (21 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l23 (10 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l9 (16 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
70s-dnax complex (Complex from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s5 (16 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s11 (12 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Iron/sulfur cluster (351 Da, Ligand)
30s ribosomal protein s10 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s7 (17 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
16s rrna (493 kDa, RNA from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s19 (9 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s8 (15 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l31 (8 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))

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EMD-8597

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70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("out" conformation)

Release date: March 7, 2018
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 5uq8
Q-score: 0.446

Zhang Y, Hong S, Ruangprasert A, Skiniotis G, Dunham CM

Structure (2018) 26 pp. 437-445.e3 [ Pubmed: 29456023 DOI: doi:10.1016/j.str.2018.01.013 ]

Sample:

5s rrna (38 kDa, RNA from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s2 (26 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s13 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l15 (16 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l22 (12 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l36 (4 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l4 (22 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s6 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l19 (15 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l30 (6 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l5 (20 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s15 (10 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
23s rrna (948 kDa, RNA from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s17 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l33 (6 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
P-site trna fmet (24 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l20 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l28 (10 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s12 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s16 (9 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l14 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l2 (30 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l34 (5 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l27 (8 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l6 (18 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein thx (2 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l18 (12 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l21 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l17 (13 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Messenger rna (17 kDa, RNA from synthetic construct)
50s ribosomal protein l13 (15 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s14 type z (7 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
E-site trna phe (24 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l24 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s18 (7 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l35 (7 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s3 (22 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l32 (6 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l1 (24 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s20 (10 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s4 (24 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l3 (22 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l16 (15 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s9 (14 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Zinc ion (65 Da, Ligand)
50s ribosomal protein l29 (8 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l25 (21 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l23 (10 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l9 (16 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
70s-dnax complex (Complex from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s5 (16 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s11 (12 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Iron/sulfur cluster (351 Da, Ligand)
30s ribosomal protein s10 (11 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s7 (17 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
16s rrna (493 kDa, RNA from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s19 (9 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
30s ribosomal protein s8 (15 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
50s ribosomal protein l31 (8 kDa, Protein from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))

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EMDB [6]

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