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!

Edit your search query here and hit Return to execute it:
grant_code:"18J11653"

Filter By

Current Database

  • EMDB [9]

Current status

  • REL [9]

Sample type

  • Complex [8]
  • Ligand [5]
  • Protein [5]
  • Cellular component [1]

Organism

  • Thermococcus profundus [9]

EM Method

  • Single-particle [9]

Resolution

  • ≥ 2Å and < 3Å [5]
  • ≥ 3Å and < 4Å [4]

Model molecular weight

  • 0-50 kDa [9]

Release Date

  • 2024 [5]
  • 2020 [4]

Author by name

  • Nakasako M [9]
  • Matsui Y [5]
  • Wakabayashi T [5]
  • Kato T [4]
  • Oide M [4]
  • Oroguchi T [4]

Author by ORCID

  • Nakasako M [9]

Journal

  • FEBS J [9]

Software

  • CTFFIND [5]
  • RELION [5]

Microscope

  • JEOL CRYO ARM 300 [5]
  • JEOL CRYO ARM 200 [4]

Electron Source

  • FIELD EMISSION GUN [9]

Film or detector model

  • GATAN K3 6K X 4K [5]
  • GATAN K2 BASE 4K X 4K [4]

External links

  • PDB [9]
  • AlphaFold DB [5]
  • ChEBI [5]
  • ChEMBL [5]
  • DrugBank [5]
  • Gene Ontology [5]
  • InterPro [5]
  • PDBe-Kb [5]
  • Pfam [5]
  • UniProt [5]
Sort by: Download
Showing 1 - 9 of 9. Page 1 of 1
Display:
Statistics
×

Download











































Preview first 10
Download
EMD-60269
Download Map
3D View
Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus in complex with NADP and GLU in the steady stage of reaction
Release date: June 26, 2024
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8zne
Q-score: 0.596

Wakabayashi T, Matsui Y, Nakasako M

FEBS J (2025) 292 pp. 2071-2094 [ DOI: doi:10.1111/febs.17415 Pubmed: 39891504 ]

EMD-60266
Download Map
3D View
Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH in the steady stage of reaction
Release date: June 12, 2024
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8znb
Q-score: 0.6

Wakabayashi T, Matsui Y, Nakasako M

FEBS J (2025) 292 pp. 2071-2094 [ DOI: doi:10.1111/febs.17415 Pubmed: 39891504 ]

EMD-60267
Download Map
3D View
Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH, AKG in the steady stage of reaction
Release date: June 12, 2024
Resolution: 2.41 Å
EM Method: Single-particle
Fitted PDBs: 8znc
Q-score: 0.625

Wakabayashi T, Matsui Y, Nakasako M

FEBS J (2025) 292 pp. 2071-2094 [ DOI: doi:10.1111/febs.17415 Pubmed: 39891504 ]

EMD-60268
Download Map
3D View
Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH and a substrate in the steady stage of reaction
Release date: June 12, 2024
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8znd
Q-score: 0.639

Wakabayashi T, Matsui Y, Nakasako M

FEBS J (2025) 292 pp. 2071-2094 [ DOI: doi:10.1111/febs.17415 Pubmed: 39891504 ]

EMD-60270
Download Map
3D View
Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH and AKG in the steady stage of reaction
Release date: June 12, 2024
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8zng
Q-score: 0.646

Wakabayashi T, Matsui Y, Nakasako M

FEBS J (2025) 292 pp. 2071-2094 [ DOI: doi:10.1111/febs.17415 Pubmed: 39891504 ]

EMD-9845
Download Map
3D View
Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus
Release date: Feb. 12, 2020
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6jn9
Q-score: 0.423

Oide M, Kato T, Oroguchi T, Nakasako M

FEBS J (2020) 287 pp. 3472-3493 [ Pubmed: 31976609 DOI: doi:10.1111/febs.15224 ]

EMD-9846
Download Map
3D View
Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus
Release date: Feb. 12, 2020
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6jna
Q-score: 0.423

Oide M, Kato T, Oroguchi T, Nakasako M

FEBS J (2020) 287 pp. 3472-3493 [ Pubmed: 31976609 DOI: doi:10.1111/febs.15224 ]

EMD-9847
Download Map
3D View
Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus
Release date: Feb. 12, 2020
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6jnc
Q-score: 0.452

Oide M, Kato T, Oroguchi T, Nakasako M

FEBS J (2020) 287 pp. 3472-3493 [ Pubmed: 31976609 DOI: doi:10.1111/febs.15224 ]

EMD-9848
Download Map
3D View
Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus
Release date: Feb. 12, 2020
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6jnd
Q-score: 0.409

Oide M, Kato T, Oroguchi T, Nakasako M

FEBS J (2020) 287 pp. 3472-3493 [ Pubmed: 31976609 DOI: doi:10.1111/febs.15224 ]

Sort by: Download
Showing 1 - 9 of 9. Page 1 of 1
Display:
Statistics
×

Download











































Preview first 10
Download

Filter By

Current Database

  • EMDB [9]

Current status

  • REL [9]

Sample type

  • Complex [8]
  • Ligand [5]
  • Protein [5]
  • Cellular component [1]

Organism

  • Thermococcus profundus [9]

EM Method

  • Single-particle [9]

Resolution

  • ≥ 2Å and < 3Å [5]
  • ≥ 3Å and < 4Å [4]

Model molecular weight

  • 0-50 kDa [9]

Release Date

  • 2024 [5]
  • 2020 [4]

Author by name

  • Nakasako M [9]
  • Matsui Y [5]
  • Wakabayashi T [5]
  • Kato T [4]
  • Oide M [4]
  • Oroguchi T [4]

Author by ORCID

  • Nakasako M [9]

Journal

  • FEBS J [9]

Software

  • CTFFIND [5]
  • RELION [5]

Microscope

  • JEOL CRYO ARM 300 [5]
  • JEOL CRYO ARM 200 [4]

Electron Source

  • FIELD EMISSION GUN [9]

Film or detector model

  • GATAN K3 6K X 4K [5]
  • GATAN K2 BASE 4K X 4K [4]

External links

  • PDB [9]
  • AlphaFold DB [5]
  • ChEBI [5]
  • ChEMBL [5]
  • DrugBank [5]
  • Gene Ontology [5]
  • InterPro [5]
  • PDBe-Kb [5]
  • Pfam [5]
  • UniProt [5]