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author:"Ishihara K"

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Current Database

  • EMDB [8]
  • EMPIAR [4]

Current status

  • REL [12]

Sample type

  • Cell [4]
  • Complex [4]
  • DNA [4]
  • Protein [4]
  • RNA [4]
  • Ligand [3]

Organism

  • Homo sapiens [4]
  • Vibrio parahaemolyticus [3]
  • Pyrococcus furiosus [1]
  • Archaeoglobus fulgidus [1]
  • Synthetic construct [1]
  • Vibrio alginolyticus [1]

EM Method

  • Single-particle [4]
  • Tomography [4]

Resolution

  • ≥ 2Å and < 3Å [3]
  • ≥ 3Å and < 4Å [1]

Model molecular weight

  • 250-500 kDa [3]
  • 500-1000 kDa [1]

Release Date

  • 2026 [3]
  • 2025 [1]
  • 2024 [8]

Author by name

  • Bragulat-teixidor H [8]
  • Ishihara K [8]
  • Otsuka S [8]
  • Numata T [4]
  • Szucs GM [4]
  • Gerle C [3]
  • Gopalasingam CC [3]
  • Matsumoto S [3]
  • Shigematsu H [3]
  • Shirai T [3]
  • Adachi N [1]
  • Akutsu M [1]
  • Inanaga H [1]
  • Kitagawa S [1]
  • Senda T [1]

Author by ORCID

  • Numata T [4]
  • Ishihara K [4]
  • Bragulat-teixidor H [4]
  • Otsuka S [4]
  • Szucs GM [4]
  • Gerle C [3]
  • Senda T [1]
  • Adachi N [1]

Journal

  • EMBO REP [8]
  • NUCLEIC ACIDS RES [3]
  • BIOCHEM BIOPHYS RES COMMUN [1]

Software

  • CRYOSPARC [2]

Microscope

  • FEI TECNAI F20 [4]
  • JEOL CRYO ARM 300 [3]
  • FEI TALOS ARCTICA [1]

Electron Source

  • FIELD EMISSION GUN [8]

Film or detector model

  • FEI EAGLE 4K X 4K [4]
  • GATAN K3 BIOCONTINUUM 6K X 4K [3]
  • FEI FALCON III 4K X 4K [1]

EMPIAR Experiment type

  • EMDB [4]

EMPIAR Image category

  • RECONSTRUCTED VOLUMES [4]
  • TILT SERIES [4]

External links

  • PDB [8]
  • AlphaFold DB [4]
  • EMDB [4]
  • EMPIAR [4]
  • Gene Ontology [4]
  • InterPro [4]
  • UniProt [4]
  • ChEBI [3]
  • DrugBank [3]
  • PDBe-Kb [1]
  • Pfam [1]
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Showing 1 - 10 of 12. Page 1 of 2
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EMD-65338
Download Map
3D View
Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in partial R-loop state
CryoEM
Release date: Feb. 11, 2026
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 9vtp
Q-score: 0.5
Similar entry percentile: 34%

Ishihara K, Matsumoto S, Gerle C, Gopalasingam CC, Shigematsu H, Shirai T, Numata T

Nucleic Acids Res (2026) 54 [ DOI: doi:10.1093/nar/gkaf1415 Pubmed: 41495894 ]

EMD-65339
Download Map
3D View
Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in full R-loop state 1
CryoEM
Release date: Feb. 11, 2026
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 9vtq
Q-score: 0.515
Similar entry percentile: 53%

Ishihara K, Matsumoto S, Gerle C, Gopalasingam CC, Shigematsu H, Shirai T, Numata T

Nucleic Acids Res (2026) 54 [ DOI: doi:10.1093/nar/gkaf1415 Pubmed: 41495894 ]

EMD-65340
Download Map
3D View
Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in full R-loop state 2
CryoEM
Release date: Feb. 11, 2026
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 9vtr
Q-score: 0.496
Similar entry percentile: 44%

Ishihara K, Matsumoto S, Gerle C, Gopalasingam CC, Shigematsu H, Shirai T, Numata T

Nucleic Acids Res (2026) 54 [ DOI: doi:10.1093/nar/gkaf1415 Pubmed: 41495894 ]

EMD-66472
Download Map
3D View
Target analog-bound type III-B Cmr complex of Archaeoglobus fulgidus
CryoEM
Release date: Dec. 10, 2025
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9x25
Q-score: 0.447
Similar entry percentile: 48%

Ishihara K, Kitagawa S, Adachi N, Akutsu M, Senda T, Inanaga H, Numata T

Biochem Biophys Res Commun (2025) 792 pp. 152978-152978 [ DOI: doi:10.1016/j.bbrc.2025.152978 Pubmed: 41242302 ]

EMPIAR-12025
Related EMDB
EMD-50068
Tomograms and the raw 2d tilt series of ER-nuclear envelope junctions of HeLa cells in interphase
Release date: July 4, 2024
Dataset size: 434.0 GB
Experiment type: EMDB

Bragulat-Teixidor H, Ishihara K, Szücs GM, Otsuka S

EMBO Rep (2024) [ Pubmed: 38877171 DOI: 10.1038/s44319-024-00175-w ]

Image sets:
  • Tilt series of ER-nuclear envelope junctions of HeLa cells in interphase
  • Reconstructed tomograms of ER-nuclear envelope junctions of HeLa cells in interphase
EMPIAR-12048
Related EMDB
EMD-50110
Tomograms and the raw 2d tilt series of ER-nuclear envelope junctions of HeLa cells in early telophase
Release date: July 4, 2024
Dataset size: 334.1 GB
Experiment type: EMDB

Bragulat-Teixidor H, Ishihara K, Szücs GM, Otsuka S

EMBO Rep (2024) [ Pubmed: 38877171 DOI: 10.1038/s44319-024-00175-w ]

Image sets:
  • Tilt series of ER-nuclear envelope junctions of HeLa cells in early telophase
  • Reconstructed tomograms of ER-nuclear envelope junctions of HeLa cells in early telophase
EMPIAR-12050
Related EMDB
EMD-50115
Tomograms and the raw 2d tilt series of ER-ER junctions of HeLa cells in interphase
Release date: July 4, 2024
Dataset size: 304.4 GB
Experiment type: EMDB

Bragulat-Teixidor H, Ishihara K, Szücs GM, Otsuka S

EMBO Rep (2024) [ Pubmed: 38877171 DOI: 10.1038/s44319-024-00175-w ]

Image sets:
  • Tilt series of ER-ER junctions of HeLa cells in interphase
  • Reconstructed tomograms of ER-ER junctions of HeLa cells in interphase
EMPIAR-12051
Related EMDB
EMD-50134
Tomograms and the raw 2d tilt series of ER-ER/nuclear envelope junctions of HeLa cells in late anaphase
Release date: July 4, 2024
Dataset size: 305.3 GB
Experiment type: EMDB

Bragulat-Teixidor H, Ishihara K, Szücs GM, Otsuka S

EMBO Rep (2024) [ Pubmed: 38877171 DOI: 10.1038/s44319-024-00175-w ]

Image sets:
  • Reconstructed tomograms of ER-ER/nuclear envelope junctions of HeLa cells in late anaphase
  • Tilt series of ER-ER/nuclear envelope junctions of HeLa cells in late anaphase
EMD-50068
Download Map
3D View
Raw data
EMPIAR-12025
Electron tomogram of ER-nuclear envelope junction of HeLa cell in interphase
Negative staining
CryoEM
Release date: June 19, 2024
EM Method: Tomography

Bragulat-Teixidor H, Ishihara K, Szucs GM, Otsuka S

EMBO Rep (2024) [ DOI: doi:10.1038/s44319-024-00175-w Pubmed: 38877171 ]

EMD-50110
Download Map
3D View
Raw data
EMPIAR-12048
Electron tomogram of ER-nuclear envelope junction of HeLa cell in early telophase
Negative staining
CryoEM
Release date: June 19, 2024
EM Method: Tomography

Bragulat-Teixidor H, Ishihara K, Szucs GM, Otsuka S

EMBO Rep (2024) [ DOI: doi:10.1038/s44319-024-00175-w Pubmed: 38877171 ]

Sort by: Download
Showing 1 - 10 of 12. Page 1 of 2
Display:
Statistics
×

Download



Preview 10 entries View All Download file

Filter By

Current Database

  • EMDB [8]
  • EMPIAR [4]

Current status

  • REL [12]

Sample type

  • Cell [4]
  • Complex [4]
  • DNA [4]
  • Protein [4]
  • RNA [4]
  • Ligand [3]

Organism

  • Homo sapiens [4]
  • Vibrio parahaemolyticus [3]
  • Pyrococcus furiosus [1]
  • Archaeoglobus fulgidus [1]
  • Synthetic construct [1]
  • Vibrio alginolyticus [1]

EM Method

  • Single-particle [4]
  • Tomography [4]

Resolution

  • ≥ 2Å and < 3Å [3]
  • ≥ 3Å and < 4Å [1]

Model molecular weight

  • 250-500 kDa [3]
  • 500-1000 kDa [1]

Release Date

  • 2026 [3]
  • 2025 [1]
  • 2024 [8]

Author by name

  • Bragulat-teixidor H [8]
  • Ishihara K [8]
  • Otsuka S [8]
  • Numata T [4]
  • Szucs GM [4]
  • Gerle C [3]
  • Gopalasingam CC [3]
  • Matsumoto S [3]
  • Shigematsu H [3]
  • Shirai T [3]
  • Adachi N [1]
  • Akutsu M [1]
  • Inanaga H [1]
  • Kitagawa S [1]
  • Senda T [1]

Author by ORCID

  • Numata T [4]
  • Ishihara K [4]
  • Bragulat-teixidor H [4]
  • Otsuka S [4]
  • Szucs GM [4]
  • Gerle C [3]
  • Senda T [1]
  • Adachi N [1]

Journal

  • EMBO REP [8]
  • NUCLEIC ACIDS RES [3]
  • BIOCHEM BIOPHYS RES COMMUN [1]

Software

  • CRYOSPARC [2]

Microscope

  • FEI TECNAI F20 [4]
  • JEOL CRYO ARM 300 [3]
  • FEI TALOS ARCTICA [1]

Electron Source

  • FIELD EMISSION GUN [8]

Film or detector model

  • FEI EAGLE 4K X 4K [4]
  • GATAN K3 BIOCONTINUUM 6K X 4K [3]
  • FEI FALCON III 4K X 4K [1]

EMPIAR Experiment type

  • EMDB [4]

EMPIAR Image category

  • RECONSTRUCTED VOLUMES [4]
  • TILT SERIES [4]

External links

  • PDB [8]
  • AlphaFold DB [4]
  • EMDB [4]
  • EMPIAR [4]
  • Gene Ontology [4]
  • InterPro [4]
  • UniProt [4]
  • ChEBI [3]
  • DrugBank [3]
  • PDBe-Kb [1]
  • Pfam [1]