Happy Holidays and New year from the EMDB! Please be advised that the EMDB team will be operating at reduced capacity between December 15th - January 12th. With this in mind we would ask that you be prepared for longer reply times through both our helpdesk system and the OneDep deposition system. well done on a productive 2025, wishing you all the best and we will see you in 2026!

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grant_code:"JP23H05475"

Filter By

Current Database

  • EMDB [56]

Current status

  • REL [56]

Sample type

  • Complex [56]
  • DNA [40]
  • Protein [40]
  • Ligand [16]
  • RNA [16]

Organism

  • Homo sapiens [54]
  • Synthetic construct [34]
  • Komagataella phaffii [7]
  • Komagataella phaffii [5]
  • Sus scrofa [3]
  • Mus musculus [2]
  • Escherichia coli [2]
  • Xenopus laevis [2]

EM Method

  • Single-particle [54]
  • Subtomogram averaging [2]

Resolution

  • ≥ 2Å and < 3Å [10]
  • ≥ 3Å and < 4Å [25]
  • ≥ 4Å and < 5Å [12]
  • ≥ 5Å and < 6Å [1]
  • ≥ 6Å and < 8Å [5]
  • ≥ 12Å and < 16Å [2]
  • ≥ 16Å and < 20Å [1]

Model molecular weight

  • 100-250 kDa [12]
  • 250-500 kDa [6]
  • 500-1000 kDa [14]
  • 1-2 MDa [8]

Release Date

  • 2025 [36]
  • 2024 [11]
  • 2023 [9]

Author by name

  • Kurumizaka H [56]
  • Takizawa Y [48]
  • Ogasawara M [34]
  • Kujirai T [31]
  • Ehara H [21]
  • Negishi L [21]
  • Hatazawa S [19]
  • Ito T [18]
  • Sekine SI [16]
  • Kato J [14]
  • Sekine S [14]
  • Kobayashi Y [12]
  • Akatsu M [11]
  • Hosoya N [9]
  • Kobayashi T [9]
  • Kobayashi W [9]
  • Oya E [9]
  • Shioi T [9]
  • Henmi M [8]
  • Hirai S [7]
  • Echigoya K [6]
  • Fujita R [6]
  • Fukuda Y [6]
  • Gotoh Y [6]
  • Kikkawa M [6]
  • Kimura H [6]
  • Kishi Y [6]
  • Masumoto H [6]
  • Saeki M [6]
  • Hashimoto K [5]
  • Iwai S [5]
  • Matsumoto S [5]
  • Ohkawa Y [5]
  • Sugasawa K [5]
  • Tachibana H [5]
  • Xu W [5]
  • Yamamoto J [5]
  • Fujii T [4]
  • Harada A [4]
  • Hayashi G [4]
  • Maehara K [4]
  • Oishi T [4]
  • Osumi K [4]
  • Yamaguchi Y [4]
  • Yamamoto K [4]
  • Aoki M [3]
  • Goto M [3]
  • Horikoshi N [3]
  • Miyake R [3]
  • Miyamoto-kohno S [3]
  • Naganuma M [3]
  • Shirouzu M [3]
  • Sogawa-fujiwara C [3]
  • Uejima T [3]
  • Hirano R [2]
  • Ho C-H [2]
  • Kimura T [2]
  • Ogasawara O [2]
  • Hirai H [1]
  • Rina H [1]

Author by ORCID

  • Kurumizaka H [46]
  • Takizawa Y [29]
  • Sekine SI [16]
  • Negishi L [15]
  • Ehara H [14]
  • Kujirai T [13]
  • Hatazawa S [13]
  • Akatsu M [11]
  • Hosoya N [9]
  • Shioi T [9]
  • Kikkawa M [6]
  • Gotoh Y [6]
  • Kimura H [6]
  • Kishi Y [6]
  • Echigoya K [6]
  • Ohkawa Y [5]
  • Sugasawa K [5]
  • Yamamoto J [5]
  • Matsumoto S [5]
  • Kobayashi Y [4]
  • Hayashi G [4]
  • Yamaguchi Y [4]
  • Maehara K [4]
  • Harada A [4]
  • Oishi T [4]
  • Goto M [3]
  • Sogawa-fujiwara C [3]
  • Shirouzu M [3]
  • Naganuma M [3]
  • Uejima T [3]
  • Ito T [3]
  • Henmi M [3]
  • Hirano R [2]
  • Ho C-H [2]
  • Ogasawara M [2]

Journal

  • NAT COMMUN [12]
  • NATURE [9]
  • GENES CELLS [8]
  • TO BE PUBLISHED [7]
  • NAT STRUCT MOL BIOL [6]
  • J BIOL CHEM [4]
  • NUCLEIC ACIDS RES [4]
  • SCI ADV [3]
  • EMBO J [2]
  • J.BIOCHEM. [1]

Software

  • RELION [14]
  • CRYOSPARC [2]
  • PYTOM [2]

Microscope

  • TFS KRIOS [29]
  • FEI TITAN KRIOS [27]

Electron Source

  • FIELD EMISSION GUN [56]

Film or detector model

  • GATAN K3 BIOQUANTUM 6K X 4K [53]
  • GATAN K3 6K X 4K [3]

External links

  • AlphaFold DB [40]
  • PDB [40]
  • PDBe-Kb [40]
  • Pfam [40]
  • UniProt [40]
  • Gene Ontology [34]
  • InterPro [33]
  • Complex Portal [30]
  • ChEBI [16]
  • ChEMBL [16]
  • DrugBank [16]
Sort by: Download
Showing 1 - 10 of 56. Page 1 of 6
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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-65715
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3D View
Cryo-EM map of the nucleosome reconstituted in E. coli cells
Release date: Dec. 10, 2025
Resolution: 2.56 Å
EM Method: Single-particle

Ho C-H, Kobayashi Y, Ogasawara O, Takizawa Y, Kurumizaka H

To Be Published

EMD-65716
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3D View
Cryo-EM structure of the close-packed di-hexasome CPDH
Release date: Dec. 10, 2025
Resolution: 4.94 Å
EM Method: Single-particle
Fitted PDBs: 9w74
Q-score: 0.224

Ho C-H, Kobayashi Y, Ogasawara O, Takizawa Y, Kurumizaka H

To Be Published

EMD-61242
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3D View
Cryo-EM structure of native NCP-UV-DDB complex
Release date: Nov. 19, 2025
Resolution: 12.3 Å
EM Method: Single-particle

Matsumoto S, Takizawa Y, Ogasawara M, Hashimoto K, Negishi L, Xu W, Tachibana H, Yamamoto J, Iwai S, Sugasawa K, Kurumizaka H

Nat Commun (2025) 16 pp. 9709-9709 [ Pubmed: 41219227 DOI: doi:10.1038/s41467-025-65486-5 ]

EMD-61243
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3D View
Cryo-EM structure of NCP-UV-DDB complex containing CPD
Release date: Nov. 19, 2025
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 9j8w
Q-score: 0.397

Matsumoto S, Takizawa Y, Ogasawara M, Hashimoto K, Negishi L, Xu W, Tachibana H, Yamamoto J, Iwai S, Sugasawa K, Kurumizaka H

Nat Commun (2025) 16 pp. 9709-9709 [ Pubmed: 41219227 DOI: doi:10.1038/s41467-025-65486-5 ]

EMD-61246
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3D View
Cryo-EM structure of UV-DDB bound to native NCP at SHL /-2
Release date: Nov. 19, 2025
Resolution: 3.78 Å
EM Method: Single-particle

Matsumoto S, Takizawa Y, Ogasawara M, Hashimoto K, Negishi L, Xu W, Tachibana H, Yamamoto J, Iwai S, Sugasawa K, Kurumizaka H

Nat Commun (2025) 16 pp. 9709-9709 [ Pubmed: 41219227 DOI: doi:10.1038/s41467-025-65486-5 ]

Sort by: Download
Showing 1 - 10 of 56. Page 1 of 6
Display:
Statistics
×

Download











































Preview first 10
Download

Filter By

Current Database

  • EMDB [56]

Current status

  • REL [56]

Sample type

  • Complex [56]
  • DNA [40]
  • Protein [40]
  • Ligand [16]
  • RNA [16]

Organism

  • Homo sapiens [54]
  • Synthetic construct [34]
  • Komagataella phaffii [7]
  • Komagataella phaffii [5]
  • Sus scrofa [3]
  • Mus musculus [2]
  • Escherichia coli [2]
  • Xenopus laevis [2]

EM Method

  • Single-particle [54]
  • Subtomogram averaging [2]

Resolution

  • ≥ 2Å and < 3Å [10]
  • ≥ 3Å and < 4Å [25]
  • ≥ 4Å and < 5Å [12]
  • ≥ 5Å and < 6Å [1]
  • ≥ 6Å and < 8Å [5]
  • ≥ 12Å and < 16Å [2]
  • ≥ 16Å and < 20Å [1]

Model molecular weight

  • 100-250 kDa [12]
  • 250-500 kDa [6]
  • 500-1000 kDa [14]
  • 1-2 MDa [8]

Release Date

  • 2025 [36]
  • 2024 [11]
  • 2023 [9]

Author by name

  • Kurumizaka H [56]
  • Takizawa Y [48]
  • Ogasawara M [34]
  • Kujirai T [31]
  • Ehara H [21]
  • Negishi L [21]
  • Hatazawa S [19]
  • Ito T [18]
  • Sekine SI [16]
  • Kato J [14]
  • Sekine S [14]
  • Kobayashi Y [12]
  • Akatsu M [11]
  • Hosoya N [9]
  • Kobayashi T [9]
  • Kobayashi W [9]
  • Oya E [9]
  • Shioi T [9]
  • Henmi M [8]
  • Hirai S [7]
  • Echigoya K [6]
  • Fujita R [6]
  • Fukuda Y [6]
  • Gotoh Y [6]
  • Kikkawa M [6]
  • Kimura H [6]
  • Kishi Y [6]
  • Masumoto H [6]
  • Saeki M [6]
  • Hashimoto K [5]
  • Iwai S [5]
  • Matsumoto S [5]
  • Ohkawa Y [5]
  • Sugasawa K [5]
  • Tachibana H [5]
  • Xu W [5]
  • Yamamoto J [5]
  • Fujii T [4]
  • Harada A [4]
  • Hayashi G [4]
  • Maehara K [4]
  • Oishi T [4]
  • Osumi K [4]
  • Yamaguchi Y [4]
  • Yamamoto K [4]
  • Aoki M [3]
  • Goto M [3]
  • Horikoshi N [3]
  • Miyake R [3]
  • Miyamoto-kohno S [3]
  • Naganuma M [3]
  • Shirouzu M [3]
  • Sogawa-fujiwara C [3]
  • Uejima T [3]
  • Hirano R [2]
  • Ho C-H [2]
  • Kimura T [2]
  • Ogasawara O [2]
  • Hirai H [1]
  • Rina H [1]

Author by ORCID

  • Kurumizaka H [46]
  • Takizawa Y [29]
  • Sekine SI [16]
  • Negishi L [15]
  • Ehara H [14]
  • Kujirai T [13]
  • Hatazawa S [13]
  • Akatsu M [11]
  • Hosoya N [9]
  • Shioi T [9]
  • Kikkawa M [6]
  • Gotoh Y [6]
  • Kimura H [6]
  • Kishi Y [6]
  • Echigoya K [6]
  • Ohkawa Y [5]
  • Sugasawa K [5]
  • Yamamoto J [5]
  • Matsumoto S [5]
  • Kobayashi Y [4]
  • Hayashi G [4]
  • Yamaguchi Y [4]
  • Maehara K [4]
  • Harada A [4]
  • Oishi T [4]
  • Goto M [3]
  • Sogawa-fujiwara C [3]
  • Shirouzu M [3]
  • Naganuma M [3]
  • Uejima T [3]
  • Ito T [3]
  • Henmi M [3]
  • Hirano R [2]
  • Ho C-H [2]
  • Ogasawara M [2]

Journal

  • NAT COMMUN [12]
  • NATURE [9]
  • GENES CELLS [8]
  • TO BE PUBLISHED [7]
  • NAT STRUCT MOL BIOL [6]
  • J BIOL CHEM [4]
  • NUCLEIC ACIDS RES [4]
  • SCI ADV [3]
  • EMBO J [2]
  • J.BIOCHEM. [1]

Software

  • RELION [14]
  • CRYOSPARC [2]
  • PYTOM [2]

Microscope

  • TFS KRIOS [29]
  • FEI TITAN KRIOS [27]

Electron Source

  • FIELD EMISSION GUN [56]

Film or detector model

  • GATAN K3 BIOQUANTUM 6K X 4K [53]
  • GATAN K3 6K X 4K [3]

External links

  • AlphaFold DB [40]
  • PDB [40]
  • PDBe-Kb [40]
  • Pfam [40]
  • UniProt [40]
  • Gene Ontology [34]
  • InterPro [33]
  • Complex Portal [30]
  • ChEBI [16]
  • ChEMBL [16]
  • DrugBank [16]