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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:"Histone H3" AND xref_links:"chembl" AND database:"EMDB" AND author_name:"Nogales"

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EMD-43361

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PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged

Release date: Jan. 22, 2025
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vnv
Q-score: 0.357

Cookis T, Lydecker A, Sauer P, Kasinath V, Nogales E

Nat Struct Mol Biol (2025) [ Pubmed: 39774834 DOI: doi:10.1038/s41594-024-01452-x ]

Sample:

Prc2_aj1-450 bound to h3k36me3 modified nucleosome with tail engaged (Complex from Homo sapiens)
Isoform 2 of histone-lysine n-methyltransferase ezh2 (85 kDa, Protein from Homo sapiens)
Protein jumonji (49 kDa, Protein from Homo sapiens)
Zinc finger protein aebp2 (31 kDa, Protein from Homo sapiens)
Eed (50 kDa, Protein from Homo sapiens)
Dna (26-mer) (8 kDa, DNA from Homo sapiens)
S-adenosyl-l-homocysteine (384 Da, Ligand)
Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
Rbap48 (47 kDa, Protein from Homo sapiens)
Dna (26-mer) (7 kDa, DNA from Homo sapiens)
H3k36me3-modified histone h3 (2 kDa, Protein from Homo sapiens)

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EMD-43357

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PRC2_AJ119-450 bound to H3K4me3

Release date: Jan. 15, 2025
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vmi
Q-score: 0.48

Cookis T, Lydecker A, Sauer P, Kasinath V, Nogales E

Nat Struct Mol Biol (2025) [ Pubmed: 39774834 DOI: doi:10.1038/s41594-024-01452-x ]

Sample:

Zinc ion (65 Da, Ligand)
Histone h3.1 (747 Da, Protein from Homo sapiens)
Polycomb protein suz12 (83 kDa, Protein from Homo sapiens)
Protein jumonji (138 kDa, Protein from Homo sapiens)
Histone h3.1t (1 kDa, Protein from Homo sapiens)
Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
Ezh2 (85 kDa, Protein from Homo sapiens)
Isoform 3 of zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
Polycomb protein eed (50 kDa, Protein from Homo sapiens)
Prc2_aj119-450 bound to h3k4me3-modified nucleosome (350 kDa, Complex from Homo sapiens)

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EMD-41110

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Automethylated PRC2 dimer bound to nucleosome

Release date: Sept. 25, 2024
Resolution: 6.2 Å
EM Method: Single-particle
Fitted PDBs: 8t9g
Q-score: 0.163

Sauer PV, Pavlenko E, Cookis T, Zirden LC, Renn J, Singhal A, Hunold P, Hoehne-Wiechmann MN, van Ray O, Kaschani F, Kaiser M, Hansel-Hertsch R, Sanbonmatsu KY, Nogales E, Poepsel S

Mol Cell (2024) 84 pp. 3885-3898.e8 [ Pubmed: 39303719 DOI: doi:10.1016/j.molcel.2024.08.025 ]

Sample:

Proximal prc2 (Complex from Homo sapiens)
Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
Distal prc2 (Complex from Homo sapiens)
Dna (226-mer) (65 kDa, DNA from synthetic construct)
Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
Activating methylated peptide (1 kDa, Protein from Homo sapiens)
S-adenosyl-l-homocysteine (384 Da, Ligand)
Histone h4 (11 kDa, Protein from Xenopus laevis)
Polycomb protein eed (50 kDa, Protein from Homo sapiens)
Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
Dna (226-mer) (66 kDa, DNA from synthetic construct)
Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Automethylated prc2 dimer bound to nucleosome (290 kDa, Complex from Homo sapiens)
Nucleosome (Complex from Xenopus laevis)

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EMD-41141

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PRC2 monomer bound to nucleosome

Release date: Sept. 25, 2024
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8tas
Q-score: 0.259

Sauer PV, Pavlenko E, Cookis T, Zirden LC, Renn J, Singhal A, Hunold P, Hoehne-Wiechmann MN, van Ray O, Kaschani F, Kaiser M, Hansel-Hertsch R, Sanbonmatsu KY, Nogales E, Poepsel S

Mol Cell (2024) 84 pp. 3885-3898.e8 [ Pubmed: 39303719 DOI: doi:10.1016/j.molcel.2024.08.025 ]

Sample:

Dna (226-mer) (65 kDa, DNA from synthetic construct)
Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
S-adenosyl-l-homocysteine (384 Da, Ligand)
Histone h4 (11 kDa, Protein from Xenopus laevis)
Polycomb protein eed (50 kDa, Protein from Homo sapiens)
Dna (226-mer) (66 kDa, DNA from synthetic construct)
Histone h2a (14 kDa, Protein from Xenopus laevis)
Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Nucleosome (Complex from Xenopus laevis)
Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Prc2 monomer bound to nucleosome (290 kDa, Complex from Homo sapiens)
Prc2 (Complex from Homo sapiens)

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EMD-41146

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PRC2-J119-450 monomer bound to H1-nucleosome

Release date: Sept. 25, 2024
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8tb9
Q-score: 0.261

Sauer PV, Pavlenko E, Cookis T, Zirden LC, Renn J, Singhal A, Hunold P, Hoehne-Wiechmann MN, van Ray O, Kaschani F, Kaiser M, Hansel-Hertsch R, Sanbonmatsu KY, Nogales E, Poepsel S

Mol Cell (2024) 84 pp. 3885-3898.e8 [ Pubmed: 39303719 DOI: doi:10.1016/j.molcel.2024.08.025 ]

Sample:

Protein jumonji (36 kDa, Protein from Homo sapiens)
Dna (226-mer) (65 kDa, DNA from synthetic construct)
Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
Histone h1.0 (21 kDa, Protein from Homo sapiens)
Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
Prc2-j119-450 monomer bound to h1-nucleosome (290 kDa, Complex from Homo sapiens)
Prc2 (Complex from Homo sapiens)
S-adenosyl-l-homocysteine (384 Da, Ligand)
Histone h4 (11 kDa, Protein from Xenopus laevis)
Polycomb protein eed (50 kDa, Protein from Homo sapiens)
Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
Dna (226-mer) (66 kDa, DNA from synthetic construct)
Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Nucleosome (Complex from Xenopus laevis)

[Show more]

EMD-21707

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PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome

Release date: Feb. 3, 2021
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6wkr
Q-score: 0.362

Kasinath V, Beck C, Sauer P, Poepsel S, Kosmatka J, Faini M, Toso D, Aebersold R, Nogales E

Science (2021) 371 [ DOI: doi:10.1126/science.abc3393 Pubmed: 33479123 ]

Sample:

Dna (314-mer) (98 kDa, DNA from Homo sapiens)
Prc2-aebp2-jarid2 (Complex from Homo sapiens)
Polycomb protein suz12 (83 kDa, Protein from Homo sapiens)
Protein jumonji (49 kDa, Protein from Homo sapiens)
Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
Zinc ion (65 Da, Ligand)
Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
H2ak119ub1 nucleosome (Complex from Xenopus laevis)
S-adenosyl-l-homocysteine (384 Da, Ligand)
Prc2-aebp2-jarid2 bound to h2ak119ub1 nucleosome (500 kDa, Complex)
Polycomb protein eed (50 kDa, Protein from Homo sapiens)
Zinc finger protein aebp2 (33 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Xenopus laevis)
Magnesium ion (24 Da, Ligand)
Histone-lysine n-methyltransferase ezh2 (85 kDa, Protein from Homo sapiens)
Ubiquitin (8 kDa, Protein from Homo sapiens)
Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)

[Show more]

EMD-21114

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Release date: Jan. 15, 2020
Resolution: 20.0 Å
EM Method: Single-particle
Fitted PDBs: 6v92
Q-score: 0.053

Patel AB, Moore CM, Greber BJ, Luo J, Zukin SA, Ranish J, Nogales E

eLife (2019) 8 [ Pubmed: 31886770 DOI: doi:10.7554/eLife.54449 ]

Sample:

Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Unknown protein (1 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Chromatin structure-remodeling complex protein rsc14 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Unknown protein (1 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Uuknown protein (1 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Histone h4 (11 kDa, Protein from Homo sapiens)
Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Rsc-ncp complex (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Unknown protein (2 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Zinc ion (65 Da, Ligand)
Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Dna (146-mer) (45 kDa, DNA from synthetic construct)
Unknown protein (4 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))

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Sort by: Download

Showing 1 - 7 of 7. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [7]

Format:

Select the script type:

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

Preview first 10

Field: