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grant_code:"JP20H03201"

Filter By

Current Database

  • EMDB [40]

Current status

  • REL [40]

Sample type

  • Complex [40]
  • DNA [35]
  • Protein [35]
  • Ligand [29]
  • RNA [29]

Organism

  • Homo sapiens [39]
  • Synthetic construct [30]
  • Komagataella phaffii [20]
  • Komagataella phaffii [5]
  • Sus scrofa [3]

EM Method

  • Single-particle [40]

Resolution

  • ≥ 2Å and < 3Å [5]
  • ≥ 3Å and < 4Å [22]
  • ≥ 4Å and < 5Å [9]
  • ≥ 5Å and < 6Å [1]
  • ≥ 6Å and < 8Å [3]

Model molecular weight

  • 100-250 kDa [3]
  • 250-500 kDa [3]
  • 500-1000 kDa [14]
  • 1-2 MDa [15]

Release Date

  • 2025 [20]
  • 2024 [2]
  • 2023 [9]
  • 2022 [9]

Author by name

  • Kujirai T [40]
  • Kurumizaka H [40]
  • Ehara H [30]
  • Sekine SI [25]
  • Takizawa Y [25]
  • Sekine S [24]
  • Ito T [18]
  • Ogasawara M [17]
  • Kato J [10]
  • Negishi L [10]
  • Shirouzu M [10]
  • Henmi M [8]
  • Osumi K [8]
  • Akatsu M [7]
  • Hirai S [7]
  • Echigoya K [6]
  • Fujita R [6]
  • Gotoh Y [6]
  • Kimura H [6]
  • Kishi Y [6]
  • Masumoto H [6]
  • Saeki M [6]
  • Ohkawa Y [5]
  • Uejima T [5]
  • Fujii T [4]
  • Harada A [4]
  • Hirano R [4]
  • Kagawa W [4]
  • Kinoshita C [4]
  • Maehara K [4]
  • Saotome M [4]
  • Yamaguchi Y [4]
  • Yamamoto K [4]
  • Aoki M [3]
  • Goto M [3]
  • Miyamoto-kohno S [3]
  • Naganuma M [3]
  • Kimura T [2]
  • Tomoya K [2]
  • Hirai H [1]
  • Rina H [1]

Author by ORCID

  • Kurumizaka H [26]
  • Sekine SI [25]
  • Ehara H [23]
  • Kujirai T [20]
  • Takizawa Y [10]
  • Negishi L [10]
  • Shirouzu M [10]
  • Akatsu M [7]
  • Gotoh Y [6]
  • Kimura H [6]
  • Kishi Y [6]
  • Echigoya K [6]
  • Ohkawa Y [5]
  • Hirano R [4]
  • Yamaguchi Y [4]
  • Maehara K [4]
  • Osumi K [4]
  • Kinoshita C [4]
  • Harada A [4]
  • Goto M [3]
  • Naganuma M [3]
  • Uejima T [3]
  • Ito T [3]
  • Henmi M [3]
  • Ogasawara M [2]

Journal

  • SCIENCE [7]
  • NAT COMMUN [6]
  • NAT STRUCT MOL BIOL [6]
  • TO BE PUBLISHED [5]
  • J BIOL CHEM [4]
  • J MOL BIOL [4]
  • SCI ADV [3]
  • EMBO J [2]
  • GENES CELLS [2]
  • J.BIOCHEM. [1]

Software

  • RELION [4]

Microscope

  • TFS KRIOS [27]
  • FEI TITAN KRIOS [13]

Electron Source

  • FIELD EMISSION GUN [40]

Film or detector model

  • GATAN K3 BIOQUANTUM 6K X 4K [37]
  • GATAN K3 6K X 4K [3]

External links

  • AlphaFold DB [35]
  • PDB [35]
  • PDBe-Kb [35]
  • Pfam [35]
  • UniProt [35]
  • Gene Ontology [30]
  • InterPro [30]
  • ChEBI [29]
  • ChEMBL [29]
  • DrugBank [29]
  • Complex Portal [23]
Sort by: Download
Showing 1 - 10 of 40. Page 1 of 4
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EMD-66103
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3D View
Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. temp115, type B
Release date: Dec. 24, 2025
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9wms
Q-score: 0.227

Kujirai T, Ehara H

To Be Published

EMD-66104
Download Map
3D View
Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. temp115, type A
Release date: Dec. 24, 2025
Resolution: 3.59 Å
EM Method: Single-particle
Fitted PDBs: 9wmt
Q-score: 0.225

Kujirai T, Ehara H

To Be Published

EMD-66105
Download Map
3D View
Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. temp130, type A
Release date: Dec. 24, 2025
Resolution: 4.28 Å
EM Method: Single-particle
Fitted PDBs: 9wmu
Q-score: 0.189

Kujirai T, Ehara H

To Be Published

EMD-66106
Download Map
3D View
Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. temp130, type B
Release date: Dec. 24, 2025
Resolution: 4.66 Å
EM Method: Single-particle
Fitted PDBs: 9wmv
Q-score: 0.168

Kujirai T, Ehara H

To Be Published

EMD-66107
Download Map
3D View
Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. temp115, FACT-hexamer
Release date: Dec. 24, 2025
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 9wmw
Q-score: 0.229

Kujirai T, Ehara H

To Be Published

EMD-60592
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3D View
RNA polymerase II elongation complex stalled at SHL -5 of the nucleosome containing histone variant H2A.B
Release date: June 11, 2025
Resolution: 4.7 Å
EM Method: Single-particle

Akatsu M, Hirano R, Kujirai T, Ogasawara M, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H

EMBO J (2025) 44 pp. 4065-4087 [ DOI: doi:10.1038/s44318-025-00473-6 Pubmed: 40447801 ]

EMD-60593
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3D View
RNA polymerase II elongation complex stalled at SHL -1 of the nucleosome containing histone variant H2A.B
Release date: June 11, 2025
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 9ii7
Q-score: 0.285

Akatsu M, Hirano R, Kujirai T, Ogasawara M, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H

EMBO J (2025) 44 pp. 4065-4087 [ DOI: doi:10.1038/s44318-025-00473-6 Pubmed: 40447801 ]

EMD-38604
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3D View
RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei
Release date: May 7, 2025
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8xrj
Q-score: 0.31

Kujirai T, Kato J, Yamamoto K, Hirai S, Fujii T, Maehara K, Harada A, Negishi L, Ogasawara M, Yamaguchi Y, Ohkawa Y, Takizawa Y, Kurumizaka H

Nat Commun (2025) 16 pp. 4724-4724 [ DOI: doi:10.1038/s41467-025-59580-x Pubmed: 40436841 ]

EMD-38607
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3D View
RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei
Release date: May 7, 2025
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8xrm
Q-score: 0.411

Kujirai T, Kato J, Yamamoto K, Hirai S, Fujii T, Maehara K, Harada A, Negishi L, Ogasawara M, Yamaguchi Y, Ohkawa Y, Takizawa Y, Kurumizaka H

Nat Commun (2025) 16 pp. 4724-4724 [ DOI: doi:10.1038/s41467-025-59580-x Pubmed: 40436841 ]

EMD-38624
Download Map
3D View
RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei
Release date: May 7, 2025
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8xso
Q-score: 0.505

Kujirai T, Kato J, Yamamoto K, Hirai S, Fujii T, Maehara K, Harada A, Negishi L, Ogasawara M, Yamaguchi Y, Ohkawa Y, Takizawa Y, Kurumizaka H

Nat Commun (2025) 16 pp. 4724-4724 [ DOI: doi:10.1038/s41467-025-59580-x Pubmed: 40436841 ]

Sort by: Download
Showing 1 - 10 of 40. Page 1 of 4
Display:
Statistics
×

Download











































Preview first 10
Download

Filter By

Current Database

  • EMDB [40]

Current status

  • REL [40]

Sample type

  • Complex [40]
  • DNA [35]
  • Protein [35]
  • Ligand [29]
  • RNA [29]

Organism

  • Homo sapiens [39]
  • Synthetic construct [30]
  • Komagataella phaffii [20]
  • Komagataella phaffii [5]
  • Sus scrofa [3]

EM Method

  • Single-particle [40]

Resolution

  • ≥ 2Å and < 3Å [5]
  • ≥ 3Å and < 4Å [22]
  • ≥ 4Å and < 5Å [9]
  • ≥ 5Å and < 6Å [1]
  • ≥ 6Å and < 8Å [3]

Model molecular weight

  • 100-250 kDa [3]
  • 250-500 kDa [3]
  • 500-1000 kDa [14]
  • 1-2 MDa [15]

Release Date

  • 2025 [20]
  • 2024 [2]
  • 2023 [9]
  • 2022 [9]

Author by name

  • Kujirai T [40]
  • Kurumizaka H [40]
  • Ehara H [30]
  • Sekine SI [25]
  • Takizawa Y [25]
  • Sekine S [24]
  • Ito T [18]
  • Ogasawara M [17]
  • Kato J [10]
  • Negishi L [10]
  • Shirouzu M [10]
  • Henmi M [8]
  • Osumi K [8]
  • Akatsu M [7]
  • Hirai S [7]
  • Echigoya K [6]
  • Fujita R [6]
  • Gotoh Y [6]
  • Kimura H [6]
  • Kishi Y [6]
  • Masumoto H [6]
  • Saeki M [6]
  • Ohkawa Y [5]
  • Uejima T [5]
  • Fujii T [4]
  • Harada A [4]
  • Hirano R [4]
  • Kagawa W [4]
  • Kinoshita C [4]
  • Maehara K [4]
  • Saotome M [4]
  • Yamaguchi Y [4]
  • Yamamoto K [4]
  • Aoki M [3]
  • Goto M [3]
  • Miyamoto-kohno S [3]
  • Naganuma M [3]
  • Kimura T [2]
  • Tomoya K [2]
  • Hirai H [1]
  • Rina H [1]

Author by ORCID

  • Kurumizaka H [26]
  • Sekine SI [25]
  • Ehara H [23]
  • Kujirai T [20]
  • Takizawa Y [10]
  • Negishi L [10]
  • Shirouzu M [10]
  • Akatsu M [7]
  • Gotoh Y [6]
  • Kimura H [6]
  • Kishi Y [6]
  • Echigoya K [6]
  • Ohkawa Y [5]
  • Hirano R [4]
  • Yamaguchi Y [4]
  • Maehara K [4]
  • Osumi K [4]
  • Kinoshita C [4]
  • Harada A [4]
  • Goto M [3]
  • Naganuma M [3]
  • Uejima T [3]
  • Ito T [3]
  • Henmi M [3]
  • Ogasawara M [2]

Journal

  • SCIENCE [7]
  • NAT COMMUN [6]
  • NAT STRUCT MOL BIOL [6]
  • TO BE PUBLISHED [5]
  • J BIOL CHEM [4]
  • J MOL BIOL [4]
  • SCI ADV [3]
  • EMBO J [2]
  • GENES CELLS [2]
  • J.BIOCHEM. [1]

Software

  • RELION [4]

Microscope

  • TFS KRIOS [27]
  • FEI TITAN KRIOS [13]

Electron Source

  • FIELD EMISSION GUN [40]

Film or detector model

  • GATAN K3 BIOQUANTUM 6K X 4K [37]
  • GATAN K3 6K X 4K [3]

External links

  • AlphaFold DB [35]
  • PDB [35]
  • PDBe-Kb [35]
  • Pfam [35]
  • UniProt [35]
  • Gene Ontology [30]
  • InterPro [30]
  • ChEBI [29]
  • ChEMBL [29]
  • DrugBank [29]
  • Complex Portal [23]