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author:"Okada Y"

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Current Database

  • EMDB [16]
  • EMPIAR [2]

Current status

  • REL [18]

Sample type

  • Protein [12]
  • Complex [11]
  • Ligand [9]
  • Cellular component [4]
  • Sample [1]

Organism

  • Homo sapiens [11]
  • Mus musculus [6]
  • Sus scrofa [5]
  • Rattus rattus [2]
  • Bos taurus [2]

EM Method

  • Single-particle [12]
  • Helical reconstruction [4]

Resolution

  • ≥ 2Å and < 3Å [9]
  • ≥ 3Å and < 4Å [1]
  • ≥ 4Å and < 5Å [1]
  • ≥ 5Å and < 6Å [1]
  • ≥ 6Å and < 8Å [3]
  • ≥ 8Å and < 12Å [1]

Model molecular weight

  • 100-250 kDa [7]
  • 500-1000 kDa [5]

Release Date

  • 2025 [1]
  • 2024 [10]
  • 2021 [1]
  • 2020 [1]
  • 2016 [4]
  • 2014 [1]

Author by name

  • Okada Y [17]
  • Nureki O [13]
  • Kusakizako T [12]
  • Itoh Y [11]
  • Kobayashi TA [11]
  • Sano FK [11]
  • Ishitani R [8]
  • Akasaka H [6]
  • Awazu T [6]
  • Hirano H [6]
  • Inoue A [6]
  • Kawakami K [6]
  • Kise Y [6]
  • Kobayashi K [6]
  • Okamoto HH [6]
  • Sako Y [6]
  • Shihoya W [6]
  • Shimizume K [6]
  • Shirouzu M [6]
  • Tanaka T [6]
  • Yanagawa M [6]
  • Enoki S [5]
  • Hirokawa N [5]
  • Nitta R [5]
  • Shimada H [5]
  • Ichimura T [4]
  • Iwamoto H [4]
  • Kambara T [4]
  • Kamimura S [4]
  • Kaneshiro J [4]
  • Morikawa M [4]
  • Shigematsu H [4]
  • Shima T [4]
  • Uemura S [4]
  • Watanabe TM [4]
  • Yagi T [4]
  • Kasuya G [2]
  • Nakamura R [2]
  • Yokoyama T [2]
  • Dohmae N [1]
  • Hagino T [1]
  • Ichijo H [1]
  • Inoue M [1]
  • Jentsch TJ [1]
  • Kato T [1]
  • Kikkawa M [1]
  • Nishizawa T [1]
  • Numata T [1]
  • Ogura T [1]
  • Sato C [1]
  • Watanabe K [1]
  • Yajima H [1]

Author by ORCID

  • Okada Y [15]
  • Kusakizako T [11]
  • Nureki O [11]
  • Itoh Y [10]
  • Sano FK [10]
  • Kobayashi TA [10]
  • Tanaka T [6]
  • Yanagawa M [6]
  • Kawakami K [6]
  • Kobayashi K [6]
  • Sako Y [6]
  • Inoue A [6]
  • Akasaka H [6]
  • Shihoya W [6]
  • Awazu T [6]
  • Nitta R [5]
  • Shima T [4]
  • Hirokawa N [4]
  • Yagi T [4]
  • Watanabe TM [4]
  • Iwamoto H [4]
  • Shigematsu H [4]
  • Sato C [1]
  • Inoue M [1]
  • Nishizawa T [1]
  • Kikkawa M [1]
  • Ogura T [1]
  • Yokoyama T [1]
  • Watanabe K [1]
  • Kato T [1]
  • Jentsch TJ [1]
  • Ichijo H [1]
  • Numata T [1]
  • Hagino T [1]
  • Shirouzu M [1]
  • Kasuya G [1]

Journal

  • NAT CHEM BIOL [6]
  • J CELL BIOL [5]
  • NAT COMMUN [5]
  • COMMUN BIOL [2]

Software

  • RELION [5]
  • FREALIGN [3]
  • CHIMERA [1]
  • MATLAB, IMAGEV [1]

Microscope

  • TFS KRIOS [6]
  • FEI TECNAI ARCTICA [4]
  • FEI TITAN KRIOS [4]
  • FEI TALOS ARCTICA [1]
  • JEOL 2010F [1]

Electron Source

  • FIELD EMISSION GUN [16]

Film or detector model

  • GATAN K3 6K X 4K [6]
  • FEI FALCON II 4K X 4K [4]
  • GATAN K3 BIOQUANTUM 6K X 4K [4]
  • GATAN K2 SUMMIT 4K X 4K [1]
  • KODAK SO-163 FILM [1]

EMPIAR Experiment type

  • EMDB [2]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [2]

External links

  • AlphaFold DB [12]
  • PDB [12]
  • PDBe-Kb [12]
  • UniProt [12]
  • Gene Ontology [11]
  • InterPro [11]
  • Pfam [11]
  • ChEBI [9]
  • ChEMBL [9]
  • DrugBank [9]
  • EMPIAR [5]
  • Complex Portal [2]
  • EMDB [2]
Sort by: Download
Showing 1 - 10 of 18. Page 1 of 2
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EMPIAR-12159
Related EMDB
EMD-36205 EMD-36206 EMD-36201 EMD-36204
Cryo-EM structures of human vitamin C transporter SVCT1
Release date: Feb. 3, 2025
Dataset size: 2.9 TB
Experiment type: EMDB

Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O

Nat. Commun. (2024) [ DOI: 10.1038/s41467-024-49899-2 Pubmed: N/A ]

Image sets:
  • Unaligned multi-frame micrographs of human SVCT1 in the substrate-free inward-open state
  • Unaligned multi-frame micrographs of human SVCT1 in the intermediate and substrate-free occluded states
  • Unaligned multi-frame micrographs of human SVCT1 in the substrate-bound inward-open state
EMD-61746
Composite map
Download Map
3D View
Cryo-EM structure of PTH-PTH1R-Gq upright state
Release date: Oct. 16, 2024
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9jr2
Q-score: 0.492

Sano FK, Shimizume K, Kobayashi K, Awazu T, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Sako Y, Yanagawa M, Inoue A, Nureki O

Nat Chem Biol (2025) [ DOI: doi:10.1038/s41589-025-01957-6 Pubmed: 40571720 ]

EMD-61747
Composite map
Download Map
3D View
Cryo-EM structure of PTH-PTH1R-Gq tilted state
Release date: Oct. 16, 2024
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9jr3
Q-score: 0.487

Sano FK, Shimizume K, Kobayashi K, Awazu T, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Sako Y, Yanagawa M, Inoue A, Nureki O

Nat Chem Biol (2025) [ DOI: doi:10.1038/s41589-025-01957-6 Pubmed: 40571720 ]

EMD-61795
Download Map
3D View
Cryo-EM structure of PTH-PTH1R-Gq complex upright state; consensus refinement
Release date: Oct. 16, 2024
Resolution: 2.76 Å
EM Method: Single-particle

Sano FK, Shimizume K, Kobayashi K, Awazu T, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Sako Y, Yanagawa M, Inoue A, Nureki O

Nat Chem Biol (2025) [ DOI: doi:10.1038/s41589-025-01957-6 Pubmed: 40571720 ]

EMD-61796
Download Map
3D View
Cryo-EM structure of PTH-PTH1R-Gq complex upright state; receptor focused refinement
Release date: Oct. 16, 2024
Resolution: 2.8 Å
EM Method: Single-particle

Sano FK, Shimizume K, Kobayashi K, Awazu T, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Sako Y, Yanagawa M, Inoue A, Nureki O

Nat Chem Biol (2025) [ DOI: doi:10.1038/s41589-025-01957-6 Pubmed: 40571720 ]

EMD-61797
Download Map
3D View
Cryo-EM structure of PTH-PTH1R-Gq complex tilted state; consensus refinement map
Release date: Oct. 16, 2024
Resolution: 2.77 Å
EM Method: Single-particle

Sano FK, Shimizume K, Kobayashi K, Awazu T, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Sako Y, Yanagawa M, Inoue A, Nureki O

Nat Chem Biol (2025) [ DOI: doi:10.1038/s41589-025-01957-6 Pubmed: 40571720 ]

EMD-61798
Download Map
3D View
Cryo-EM structure of PTH-PTH1R-Gq complex tilted state; focused refinement map
Release date: Oct. 16, 2024
Resolution: 2.75 Å
EM Method: Single-particle

Sano FK, Shimizume K, Kobayashi K, Awazu T, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Sako Y, Yanagawa M, Inoue A, Nureki O

Nat Chem Biol (2025) [ DOI: doi:10.1038/s41589-025-01957-6 Pubmed: 40571720 ]

EMD-36204
Download Map
3D View
Raw data
EMPIAR-12159
Human sodium-dependent vitamin C transporter 1 in an apo inward-open state
Release date: June 19, 2024
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8jez
Q-score: 0.616

Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O

Nat Commun (2024) 15 pp. 5569-5569 [ Pubmed: 38956111 DOI: doi:10.1038/s41467-024-49899-2 ]

EMD-36201
Download Map
3D View
Raw data
EMPIAR-12159
Human sodium-dependent vitamin C transporter 1 bound to L-ascorbic acid in an inward-open state
Release date: May 22, 2024
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 8jew

Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O

Nat Commun (2024) 15 pp. 5569-5569 [ Pubmed: 38956111 DOI: doi:10.1038/s41467-024-49899-2 ]

EMD-36205
Download Map
3D View
Raw data
EMPIAR-12159
Human sodium-dependent vitamin C transporter 1 in an intermediate state
Release date: May 22, 2024
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8jf0

Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O

Nat Commun (2024) 15 pp. 5569-5569 [ Pubmed: 38956111 DOI: doi:10.1038/s41467-024-49899-2 ]

Sort by: Download
Showing 1 - 10 of 18. Page 1 of 2
Display:
Statistics
×

Download












































Preview first 10
Download

Filter By

Current Database

  • EMDB [16]
  • EMPIAR [2]

Current status

  • REL [18]

Sample type

  • Protein [12]
  • Complex [11]
  • Ligand [9]
  • Cellular component [4]
  • Sample [1]

Organism

  • Homo sapiens [11]
  • Mus musculus [6]
  • Sus scrofa [5]
  • Rattus rattus [2]
  • Bos taurus [2]

EM Method

  • Single-particle [12]
  • Helical reconstruction [4]

Resolution

  • ≥ 2Å and < 3Å [9]
  • ≥ 3Å and < 4Å [1]
  • ≥ 4Å and < 5Å [1]
  • ≥ 5Å and < 6Å [1]
  • ≥ 6Å and < 8Å [3]
  • ≥ 8Å and < 12Å [1]

Model molecular weight

  • 100-250 kDa [7]
  • 500-1000 kDa [5]

Release Date

  • 2025 [1]
  • 2024 [10]
  • 2021 [1]
  • 2020 [1]
  • 2016 [4]
  • 2014 [1]

Author by name

  • Okada Y [17]
  • Nureki O [13]
  • Kusakizako T [12]
  • Itoh Y [11]
  • Kobayashi TA [11]
  • Sano FK [11]
  • Ishitani R [8]
  • Akasaka H [6]
  • Awazu T [6]
  • Hirano H [6]
  • Inoue A [6]
  • Kawakami K [6]
  • Kise Y [6]
  • Kobayashi K [6]
  • Okamoto HH [6]
  • Sako Y [6]
  • Shihoya W [6]
  • Shimizume K [6]
  • Shirouzu M [6]
  • Tanaka T [6]
  • Yanagawa M [6]
  • Enoki S [5]
  • Hirokawa N [5]
  • Nitta R [5]
  • Shimada H [5]
  • Ichimura T [4]
  • Iwamoto H [4]
  • Kambara T [4]
  • Kamimura S [4]
  • Kaneshiro J [4]
  • Morikawa M [4]
  • Shigematsu H [4]
  • Shima T [4]
  • Uemura S [4]
  • Watanabe TM [4]
  • Yagi T [4]
  • Kasuya G [2]
  • Nakamura R [2]
  • Yokoyama T [2]
  • Dohmae N [1]
  • Hagino T [1]
  • Ichijo H [1]
  • Inoue M [1]
  • Jentsch TJ [1]
  • Kato T [1]
  • Kikkawa M [1]
  • Nishizawa T [1]
  • Numata T [1]
  • Ogura T [1]
  • Sato C [1]
  • Watanabe K [1]
  • Yajima H [1]

Author by ORCID

  • Okada Y [15]
  • Kusakizako T [11]
  • Nureki O [11]
  • Itoh Y [10]
  • Sano FK [10]
  • Kobayashi TA [10]
  • Tanaka T [6]
  • Yanagawa M [6]
  • Kawakami K [6]
  • Kobayashi K [6]
  • Sako Y [6]
  • Inoue A [6]
  • Akasaka H [6]
  • Shihoya W [6]
  • Awazu T [6]
  • Nitta R [5]
  • Shima T [4]
  • Hirokawa N [4]
  • Yagi T [4]
  • Watanabe TM [4]
  • Iwamoto H [4]
  • Shigematsu H [4]
  • Sato C [1]
  • Inoue M [1]
  • Nishizawa T [1]
  • Kikkawa M [1]
  • Ogura T [1]
  • Yokoyama T [1]
  • Watanabe K [1]
  • Kato T [1]
  • Jentsch TJ [1]
  • Ichijo H [1]
  • Numata T [1]
  • Hagino T [1]
  • Shirouzu M [1]
  • Kasuya G [1]

Journal

  • NAT CHEM BIOL [6]
  • J CELL BIOL [5]
  • NAT COMMUN [5]
  • COMMUN BIOL [2]

Software

  • RELION [5]
  • FREALIGN [3]
  • CHIMERA [1]
  • MATLAB, IMAGEV [1]

Microscope

  • TFS KRIOS [6]
  • FEI TECNAI ARCTICA [4]
  • FEI TITAN KRIOS [4]
  • FEI TALOS ARCTICA [1]
  • JEOL 2010F [1]

Electron Source

  • FIELD EMISSION GUN [16]

Film or detector model

  • GATAN K3 6K X 4K [6]
  • FEI FALCON II 4K X 4K [4]
  • GATAN K3 BIOQUANTUM 6K X 4K [4]
  • GATAN K2 SUMMIT 4K X 4K [1]
  • KODAK SO-163 FILM [1]

EMPIAR Experiment type

  • EMDB [2]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [2]

External links

  • AlphaFold DB [12]
  • PDB [12]
  • PDBe-Kb [12]
  • UniProt [12]
  • Gene Ontology [11]
  • InterPro [11]
  • Pfam [11]
  • ChEBI [9]
  • ChEMBL [9]
  • DrugBank [9]
  • EMPIAR [5]
  • Complex Portal [2]
  • EMDB [2]