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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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* AND software_ft:"CRYOSPARC" AND resolution:[3 TO 4} AND citation_journal_name:"EMBO REP"

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EMD-18778

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Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome

Release date: Oct. 23, 2024
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8qzm
Q-score: 0.506

Wapenaar H, Clifford G, Rolls W, Pasquier M, Burdett H, Zhang Y, Deak G, Zou J, Spanos C, Taylor MRD, Mills J, Watson JA, Kumar D, Clark R, Das A, Valsakumar D, Bramham J, Voigt P, Sproul D, Wilson MD

EMBO Rep (2024) 25 pp. 5743-5779 [ Pubmed: 39528729 DOI: doi:10.1038/s44319-024-00306-3 ]

Sample:

Histone h3 (fragment) (15 kDa, Protein from Homo sapiens)
Dna (145-mer) (59 kDa, DNA from synthetic construct)
Ubiquitin (Complex from Homo sapiens)
Dna (cytosine-5)-methyltransferase 3a (102 kDa, Protein from Homo sapiens)
Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)
Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
Dna (145-mer) (60 kDa, DNA from synthetic construct)

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EMD-24385

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Structure of TRPV3 in complex with osthole

Release date: Sept. 8, 2021
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 7ras
Q-score: 0.413

Neuberger A, Nadezhdin KD, Zakharian E, Sobolevsky AI

EMBO Rep (2021) 22 pp. e53233-e53233 [ Pubmed: 34472684 DOI: doi:10.15252/embr.202153233 ]

Sample:

Sample 1 (Complex from Mus musculus)
Transient receptor potential cation channel subfamily v member 3 (92 kDa, Protein from Mus musculus)
7-methoxy-8-(3-methylbut-2-enyl)chromen-2-one (244 Da, Ligand)

EMD-24386

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Structure of TRPV3 in complex with osthole

Release date: Sept. 8, 2021
Resolution: 3.99 Å
EM Method: Single-particle
Fitted PDBs: 7rau
Q-score: 0.298

Neuberger A, Nadezhdin KD, Zakharian E, Sobolevsky AI

EMBO Rep (2021) 22 pp. e53233-e53233 [ Pubmed: 34472684 DOI: doi:10.15252/embr.202153233 ]

Sample:

Sample 1 (Complex from Mus musculus)
Transient receptor potential cation channel subfamily v member 3 (92 kDa, Protein from Mus musculus)
7-methoxy-8-(3-methylbut-2-enyl)chromen-2-one (244 Da, Ligand)

EMD-10847

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CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae

Release date: Sept. 9, 2020
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 6ymx
Q-score: 0.495

Berndtsson J, Aufschnaiter A, Rathore S, Marin-Buera L, Dawitz H, Diessl J, Kohler V, Barrientos A, Buttner S, Fontanesi F, Ott M

EMBO Rep (2020) 21 pp. e51015-e51015 [ DOI: doi:10.15252/embr.202051015 Pubmed: 33016568 ]

Sample:

Cytochrome b-c1 complex subunit 1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome b-c1 complex subunit 2, mitochondrial (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 5a, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome b (43 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome b-c1 complex subunit 6, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome b-c1 complex subunit 10, mitochondrial (5 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
(2r,5s,11r,14r)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate (834 Da, Ligand)
Cytochrome b-c1 complex subunit 6, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Fe2/s2 (inorganic) cluster (175 Da, Ligand)
Cytochrome b-c1 complex subunit 10, mitochondrial (4 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c1, heme protein, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome b-c1 complex subunit rieske, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome b-c1 complex subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Respiratroy supercopmlex ciii2/civ (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 12, mitochondrial (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
(1r)-2-{[(s)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate (593 Da, Ligand)
Phosphatidylethanolamine (734 Da, Ligand)
(1r)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate (592 Da, Ligand)
(2r)-3-{[(s)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate (691 Da, Ligand)
5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy-6-methyl-benzene-1,4-diol (592 Da, Ligand)
Cytochrome b-c1 complex subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 1 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Heme-a (852 Da, Ligand)
Cytochrome c oxidase subunit 26, mitochondrial (4 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 6, mitochondrial (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Zinc ion (65 Da, Ligand)
Protoporphyrin ix containing fe (616 Da, Ligand)
1,2-diacyl-sn-glycero-3-phoshocholine (734 Da, Ligand)
Cytochrome c oxidase subunit 13, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
(5s,11r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate (634 Da, Ligand)
Cytochrome b-c1 complex subunit 7, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 2 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome b-c1 complex subunit 8, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 7, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Copper (ii) ion (63 Da, Ligand)
(1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
Cytochrome c oxidase subunit 3 (30 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dinuclear copper ion (127 Da, Ligand)
Cytochrome c oxidase subunit 8, mitochondrial (5 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 4, mitochondrial (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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EMD-10848

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Cytochrome c oxidase from Saccharomyces cerevisiae

Release date: Sept. 9, 2020
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 6ymy
Q-score: 0.483

Berndtsson J, Aufschnaiter A, Rathore S, Marin-Buera L, Dawitz H, Diessl J, Kohler V, Barrientos A, Buttner S, Fontanesi F, Ott M

EMBO Rep (2020) 21 pp. e51015-e51015 [ DOI: doi:10.15252/embr.202051015 Pubmed: 33016568 ]

Sample:

Cytochrome c oxidase subunit 5a, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
(2r,5s,11r,14r)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate (834 Da, Ligand)
Cytochrome c oxidase subunit 12, mitochondrial (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Phosphatidylethanolamine (734 Da, Ligand)
Cytochrome c oxidase subunit 1 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Heme-a (852 Da, Ligand)
Cytochrome c oxidase subunit 26, mitochondrial (4 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 6, mitochondrial (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Zinc ion (65 Da, Ligand)
1,2-diacyl-sn-glycero-3-phoshocholine (734 Da, Ligand)
Cytochrome c oxidase (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 13, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 2 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 7, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Copper (ii) ion (63 Da, Ligand)
Cytochrome c oxidase subunit 3 (30 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dinuclear copper ion (127 Da, Ligand)
Cytochrome c oxidase subunit 8, mitochondrial (5 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cytochrome c oxidase subunit 4, mitochondrial (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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