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author:"Kobayashi TA"

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Current Database

  • EMDB [32]
  • EMPIAR [1]

Current status

  • REL [33]

Sample type

  • Complex [32]
  • Protein [28]
  • Ligand [12]
  • DNA [3]
  • RNA [3]

Organism

  • Homo sapiens [29]
  • Mus musculus [11]
  • Lachnospiraceae bacterium nd2006 [3]
  • Rattus rattus [2]
  • Bacterium [2]
  • (no species) [2]
  • Bos taurus [2]
  • Thermanaerosceptrum fracticalcis [1]
  • Dna molecule [1]

EM Method

  • Single-particle [32]

Resolution

  • ≥ 2Å and < 3Å [14]
  • ≥ 3Å and < 4Å [18]

Model molecular weight

  • 0-50 kDa [3]
  • 50-100 kDa [5]
  • 100-250 kDa [19]
  • 250-500 kDa [1]

Release Date

  • 2026 [3]
  • 2025 [20]
  • 2024 [10]

Author by name

  • Kobayashi TA [33]
  • Nureki O [33]
  • Itoh Y [30]
  • Sano FK [30]
  • Akasaka H [25]
  • Shihoya W [25]
  • Banerjee R [19]
  • Dalal A [19]
  • Ganguly M [19]
  • Mishra S [19]
  • Roy N [19]
  • Saha S [19]
  • Sharma S [19]
  • Shukla AK [19]
  • Tiwari D [19]
  • Zaidi N [19]
  • Banerjee N [13]
  • Chevigne A [13]
  • Mohapatra S [13]
  • Yadav MK [13]
  • Kusakizako T [11]
  • Okada Y [11]
  • Awazu T [6]
  • Hirano H [6]
  • Inoue A [6]
  • Ishitani R [6]
  • Kawakami K [6]
  • Kise Y [6]
  • Kobayashi K [6]
  • Leurs R [6]
  • Okamoto HH [6]
  • Sako Y [6]
  • Shimizume K [6]
  • Tanaka T [6]
  • Yanagawa M [6]
  • Enoki S [5]
  • Shimada H [5]
  • Alfonse L [3]
  • Ditommaso T [3]
  • Garrity AJ [3]
  • Koonin EV [3]
  • Maben Z [3]
  • Makarova KS [3]
  • Morinaga H [3]
  • Munoz G [3]
  • Omura SN [3]
  • Onishi K [3]
  • Ornstein A [3]
  • Shmakov SA [3]

Author by ORCID

  • Itoh Y [14]
  • Sano FK [14]
  • Nureki O [14]
  • Kobayashi TA [14]
  • Akasaka H [10]
  • Shihoya W [10]
  • Kusakizako T [8]
  • Okada Y [8]
  • Banerjee R [6]
  • Leurs R [6]
  • Shukla AK [6]
  • Sharma S [6]
  • Tanaka T [4]
  • Yanagawa M [4]
  • Kawakami K [4]
  • Kobayashi K [4]
  • Sako Y [4]
  • Inoue A [4]

Journal

  • MOL CELL [13]
  • NAT COMMUN [11]
  • NAT CHEM BIOL [6]
  • TO BE PUBLISHED [3]

Software

  • CRYOSPARC [22]
  • RELION [17]

Microscope

  • FEI TITAN KRIOS [23]
  • TFS KRIOS [9]

Electron Source

  • FIELD EMISSION GUN [32]

Film or detector model

  • GATAN K3 6K X 4K [25]
  • GATAN K3 BIOQUANTUM 6K X 4K [7]

EMPIAR Experiment type

  • EMDB [1]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [1]

External links

  • PDB [28]
  • AlphaFold DB [26]
  • Pfam [26]
  • UniProt [26]
  • Gene Ontology [25]
  • InterPro [25]
  • PDBe-Kb [25]
  • ChEBI [8]
  • ChEMBL [8]
  • Complex Portal [8]
  • DrugBank [8]
  • EMPIAR [4]
  • EMDB [1]
Sort by: Download
Showing 1 - 10 of 33. Page 1 of 4
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Preview 10 entries View All Download file
EMD-69297
Download Map
3D View
Cryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex in the TS-cleaving state
CryoEM
Release date: Sept. 2, 2026
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 23vu
Q-score: 0.623
Similar entry percentile: 91%

Morinaga H, Omura SN, Alfonse L, Ornstein A, Kobayashi TA, Onishi K, Makarova KS, Shmakov SA, Munoz G, Garrity AJ, DiTommaso T, Koonin EV, Maben Z, Nureki O

To Be Published

EMD-69298
Download Map
3D View
Cryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex in the NTS-cleaving state
CryoEM
Release date: Sept. 2, 2026
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 23vv
Q-score: 0.581
Similar entry percentile: 86%

Morinaga H, Omura SN, Alfonse L, Ornstein A, Kobayashi TA, Onishi K, Makarova KS, Shmakov SA, Munoz G, Garrity AJ, DiTommaso T, Koonin EV, Maben Z, Nureki O

To Be Published

EMD-69299
Download Map
3D View
Cryo-EM structure of the TfCas12m3-crRNA-tgDNA ternary complex
CryoEM
Release date: Sept. 2, 2026
Resolution: 2.39 Å
EM Method: Single-particle
Fitted PDBs: 23vw
Q-score: 0.629
Similar entry percentile: 80%

Morinaga H, Omura SN, Alfonse L, Ornstein A, Kobayashi TA, Onishi K, Makarova KS, Shmakov SA, Munoz G, Garrity AJ, DiTommaso T, Koonin EV, Maben Z, Nureki O

To Be Published

EMD-38765
Download Map
3D View
Structure of CXCR3 in the apo-state Receptor focused map
CryoEM
Release date: Feb. 26, 2025
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8xxy
Q-score: 0.372
Similar entry percentile: 30%

Saha S, Sano FK, Sharma S, Ganguly M, Dalal A, Mishra S, Tiwari D, Akasaka H, Kobayashi TA, Roy N, Zaidi N, Itoh Y, Leurs R, Banerjee R, Shihoya W, Nureki O, Shukla AK

Nat Commun (2025) 16 pp. 3047-3047 [ Pubmed: 40155369 DOI: doi:10.1038/s41467-025-58264-w ]

EMD-38766
Download Map
3D View
Structure of CXCR3 in the apo-state Full map
CryoEM
Release date: Feb. 26, 2025
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8xxz
Q-score: 0.464
Similar entry percentile: 52%

Saha S, Sano FK, Sharma S, Ganguly M, Dalal A, Mishra S, Tiwari D, Akasaka H, Kobayashi TA, Roy N, Zaidi N, Itoh Y, Leurs R, Banerjee R, Shihoya W, Nureki O, Shukla AK

Nat Commun (2025) 16 pp. 3047-3047 [ Pubmed: 40155369 DOI: doi:10.1038/s41467-025-58264-w ]

EMD-38774
Download Map
3D View
Structure of CXCR3 in complex with VUF10661 Receptor-ligand focused map
CryoEM
Release date: Feb. 26, 2025
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 8xyi
Q-score: 0.489
Similar entry percentile: 56%

Saha S, Sano FK, Sharma S, Ganguly M, Dalal A, Mishra S, Tiwari D, Akasaka H, Kobayashi TA, Roy N, Zaidi N, Itoh Y, Leurs R, Banerjee R, Shihoya W, Nureki O, Shukla AK

Nat Commun (2025) 16 pp. 3047-3047 [ Pubmed: 40155369 DOI: doi:10.1038/s41467-025-58264-w ]

EMD-38776
Download Map
3D View
Structure of CXCR3 in complex with VUF10661 and Go Full map
CryoEM
Release date: Feb. 26, 2025
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 8xyk
Q-score: 0.509
Similar entry percentile: 60%

Saha S, Sano FK, Sharma S, Ganguly M, Dalal A, Mishra S, Tiwari D, Akasaka H, Kobayashi TA, Roy N, Zaidi N, Itoh Y, Leurs R, Banerjee R, Shihoya W, Nureki O, Shukla AK

Nat Commun (2025) 16 pp. 3047-3047 [ Pubmed: 40155369 DOI: doi:10.1038/s41467-025-58264-w ]

EMD-38803
Download Map
3D View
Structure of CXCR3 in complex with VUF11418 Receptor-ligand focused map
CryoEM
Release date: Feb. 26, 2025
Resolution: 3.53 Å
EM Method: Single-particle
Fitted PDBs: 8y0h
Q-score: 0.433
Similar entry percentile: 49%

Saha S, Sano FK, Sharma S, Ganguly M, Dalal A, Mishra S, Tiwari D, Akasaka H, Kobayashi TA, Roy N, Zaidi N, Itoh Y, Leurs R, Banerjee R, Shihoya W, Nureki O, Shukla AK

Nat Commun (2025) 16 pp. 3047-3047 [ Pubmed: 40155369 DOI: doi:10.1038/s41467-025-58264-w ]

EMD-38809
Download Map
3D View
Structure of CXCR3 in complex with VUF11418 and Go Full map
CryoEM
Release date: Feb. 26, 2025
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8y0n
Q-score: 0.491
Similar entry percentile: 52%

Saha S, Sano FK, Sharma S, Ganguly M, Dalal A, Mishra S, Tiwari D, Akasaka H, Kobayashi TA, Roy N, Zaidi N, Itoh Y, Leurs R, Banerjee R, Shihoya W, Nureki O, Shukla AK

Nat Commun (2025) 16 pp. 3047-3047 [ Pubmed: 40155369 DOI: doi:10.1038/s41467-025-58264-w ]

EMPIAR-12159
Related EMDB
EMD-36206 EMD-36201 EMD-36205 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) [ Pubmed: N/A DOI: 10.1038/s41467-024-49899-2 ]

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
Sort by: Download
Showing 1 - 10 of 33. Page 1 of 4
Display:
Statistics
×

Download



Preview 10 entries View All Download file

Filter By

Current Database

  • EMDB [32]
  • EMPIAR [1]

Current status

  • REL [33]

Sample type

  • Complex [32]
  • Protein [28]
  • Ligand [12]
  • DNA [3]
  • RNA [3]

Organism

  • Homo sapiens [29]
  • Mus musculus [11]
  • Lachnospiraceae bacterium nd2006 [3]
  • Rattus rattus [2]
  • Bacterium [2]
  • (no species) [2]
  • Bos taurus [2]
  • Thermanaerosceptrum fracticalcis [1]
  • Dna molecule [1]

EM Method

  • Single-particle [32]

Resolution

  • ≥ 2Å and < 3Å [14]
  • ≥ 3Å and < 4Å [18]

Model molecular weight

  • 0-50 kDa [3]
  • 50-100 kDa [5]
  • 100-250 kDa [19]
  • 250-500 kDa [1]

Release Date

  • 2026 [3]
  • 2025 [20]
  • 2024 [10]

Author by name

  • Kobayashi TA [33]
  • Nureki O [33]
  • Itoh Y [30]
  • Sano FK [30]
  • Akasaka H [25]
  • Shihoya W [25]
  • Banerjee R [19]
  • Dalal A [19]
  • Ganguly M [19]
  • Mishra S [19]
  • Roy N [19]
  • Saha S [19]
  • Sharma S [19]
  • Shukla AK [19]
  • Tiwari D [19]
  • Zaidi N [19]
  • Banerjee N [13]
  • Chevigne A [13]
  • Mohapatra S [13]
  • Yadav MK [13]
  • Kusakizako T [11]
  • Okada Y [11]
  • Awazu T [6]
  • Hirano H [6]
  • Inoue A [6]
  • Ishitani R [6]
  • Kawakami K [6]
  • Kise Y [6]
  • Kobayashi K [6]
  • Leurs R [6]
  • Okamoto HH [6]
  • Sako Y [6]
  • Shimizume K [6]
  • Tanaka T [6]
  • Yanagawa M [6]
  • Enoki S [5]
  • Shimada H [5]
  • Alfonse L [3]
  • Ditommaso T [3]
  • Garrity AJ [3]
  • Koonin EV [3]
  • Maben Z [3]
  • Makarova KS [3]
  • Morinaga H [3]
  • Munoz G [3]
  • Omura SN [3]
  • Onishi K [3]
  • Ornstein A [3]
  • Shmakov SA [3]

Author by ORCID

  • Itoh Y [14]
  • Sano FK [14]
  • Nureki O [14]
  • Kobayashi TA [14]
  • Akasaka H [10]
  • Shihoya W [10]
  • Kusakizako T [8]
  • Okada Y [8]
  • Banerjee R [6]
  • Leurs R [6]
  • Shukla AK [6]
  • Sharma S [6]
  • Tanaka T [4]
  • Yanagawa M [4]
  • Kawakami K [4]
  • Kobayashi K [4]
  • Sako Y [4]
  • Inoue A [4]

Journal

  • MOL CELL [13]
  • NAT COMMUN [11]
  • NAT CHEM BIOL [6]
  • TO BE PUBLISHED [3]

Software

  • CRYOSPARC [22]
  • RELION [17]

Microscope

  • FEI TITAN KRIOS [23]
  • TFS KRIOS [9]

Electron Source

  • FIELD EMISSION GUN [32]

Film or detector model

  • GATAN K3 6K X 4K [25]
  • GATAN K3 BIOQUANTUM 6K X 4K [7]

EMPIAR Experiment type

  • EMDB [1]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [1]

External links

  • PDB [28]
  • AlphaFold DB [26]
  • Pfam [26]
  • UniProt [26]
  • Gene Ontology [25]
  • InterPro [25]
  • PDBe-Kb [25]
  • ChEBI [8]
  • ChEMBL [8]
  • Complex Portal [8]
  • DrugBank [8]
  • EMPIAR [4]
  • EMDB [1]