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:"JP19am0101117"

Filter By

Current Database

  • EMDB [26]

Current status

  • REL [26]

Sample type

  • Complex [25]
  • Protein [18]
  • Cellular component [1]
  • DNA [1]

Organism

  • Salmonella enterica [10]
  • Escherichia coli [6]
  • Salmonella enterica [6]
  • Homo sapiens [3]
  • Severe acute respiratory syndrome coronavirus [2]
  • Mus musculus [1]
  • Mycoplasma pneumoniae [1]
  • Thermus thermophilus [1]
  • Thermus thermophilus [1]
  • Synthetic construct [1]
  • Gallus gallus [1]

EM Method

  • Single-particle [26]

Resolution

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

Model molecular weight

  • 100-250 kDa [3]
  • 1-2 MDa [1]
  • 2-5 MDa [3]

Release Date

  • 2025 [6]
  • 2023 [2]
  • 2022 [10]
  • 2021 [6]
  • 2020 [2]

Author by name

  • Namba K [26]
  • Makino F [23]
  • Kato T [19]
  • Imada K [12]
  • Kinoshita M [12]
  • Minamino T [12]
  • Anzai I [11]
  • Asahara H [11]
  • Fujita J [11]
  • Inoue T [11]
  • Kishikawa J [11]
  • Kishikawa JI [11]
  • Kumano S [11]
  • Matsuura Y [11]
  • Miyata T [11]
  • Moriguchi M [11]
  • Kawamoto A [7]
  • Homma M [2]
  • Kojima S [2]
  • Sakuma M [2]
  • Takekawa N [2]
  • Aparicio D [1]
  • Ariyoshi M [1]
  • Bierge P [1]
  • Espasa M [1]
  • Esperalba J [1]
  • Fernandez-huerta M [1]
  • Fita I [1]
  • Frangakis AS [1]
  • Fukagawa T [1]
  • Horvath P [1]
  • Illanes R [1]
  • Jiang H [1]
  • Kenri T [1]
  • Lluch-senar M [1]
  • Martin J [1]
  • Matsumoto U [1]
  • Mazzolini R [1]
  • Miyata M [1]
  • Mori S [1]
  • Perez-luque R [1]
  • Pich OQ [1]
  • Pinyol J [1]
  • Sanfeliu I [1]
  • Scheffer MP [1]
  • Shibayama K [1]
  • Vizarraga D [1]
  • Watanabe R [1]

Author by ORCID

  • Namba K [13]
  • Imada K [12]
  • Anzai I [11]
  • Fujita J [11]
  • Kishikawa JI [11]
  • Minamino T [10]
  • Kinoshita M [9]
  • Makino F [6]
  • Kato T [6]
  • Miyata T [5]
  • Kawamoto A [5]
  • Kojima S [2]
  • Takekawa N [2]
  • Scheffer MP [1]
  • Horvath P [1]
  • Fukagawa T [1]
  • Ariyoshi M [1]
  • Illanes R [1]
  • Fernandez-huerta M [1]
  • Aparicio D [1]
  • Kenri T [1]
  • Vizarraga D [1]
  • Mori S [1]
  • Miyata M [1]
  • Jiang H [1]
  • Frangakis AS [1]
  • Perez-luque R [1]
  • Esperalba J [1]
  • Mazzolini R [1]
  • Pich OQ [1]
  • Espasa M [1]

Journal

  • SCI REP [11]
  • NAT COMMUN [6]
  • COMMUN BIOL [5]
  • MBIO [2]
  • BIORXIV [1]
  • PNAS [1]

Software

  • RELION [23]
  • GCTF [3]
  • WARP [3]
  • CRYOSPARC [1]

Microscope

  • JEOL CRYO ARM 300 [21]
  • FEI TITAN KRIOS [4]
  • JEOL CRYO ARM 200 [1]

Electron Source

  • FIELD EMISSION GUN [26]

Film or detector model

  • GATAN K3 6K X 4K [21]
  • FEI FALCON II 4K X 4K [3]
  • FEI FALCON III 4K X 4K [1]
  • GATAN K2 SUMMIT 4K X 4K [1]

External links

  • UniProt [16]
  • PDBe-Kb [15]
  • AlphaFold DB [13]
  • EMPIAR [11]
  • PDB [7]
  • Complex Portal [6]
  • Pfam [6]
  • Gene Ontology [5]
  • InterPro [5]
Sort by: Download
Showing 1 - 10 of 26. Page 1 of 3
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EMD-61993
Download Map
3D View
Structure of the Salmonella flagellar FliPQR complex reconstituted in the peptidisc
Release date: Aug. 6, 2025
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9k29
Q-score: 0.493

Kinoshita M, Miyata T, Makino F, Imada K, Namba K, Minamino T

PNAS (2025) 122 pp. e2507221122-e2507221122 [ Pubmed: 40833400 DOI: doi:10.1073/pnas.2507221122 ]

EMD-60007
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3D View
Structure of the Salmonella flagellar MS-ring with C11 symmetry applied
Release date: Jan. 1, 2025
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8zds
Q-score: 0.43

Kinoshita M, Makino F, Miyata T, Imada K, Namba K, Minamino T

Commun Biol (2025) 8 pp. 61-61 [ DOI: doi:10.1038/s42003-025-07485-2 Pubmed: 39820129 ]

EMD-60008
Download Map
3D View
Structure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C33 symmetry applied
Release date: Jan. 1, 2025
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8zdt
Q-score: 0.629

Kinoshita M, Makino F, Miyata T, Imada K, Namba K, Minamino T

Commun Biol (2025) 8 pp. 61-61 [ DOI: doi:10.1038/s42003-025-07485-2 Pubmed: 39820129 ]

EMD-60009
Download Map
3D View
Structure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C34 symmetry applied
Release date: Jan. 1, 2025
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8zdu
Q-score: 0.603

Kinoshita M, Makino F, Miyata T, Imada K, Namba K, Minamino T

Commun Biol (2025) 8 pp. 61-61 [ DOI: doi:10.1038/s42003-025-07485-2 Pubmed: 39820129 ]

EMD-62210
Download Map
3D View
Structure of the 34-mer RBM3 ring of Salmonella flagellar MS-ring protein FliF with C1 symmetry applied
Release date: Jan. 1, 2025
Resolution: 3.6 Å
EM Method: Single-particle

Kinoshita M, Makino F, Miyata T, Imada K, Namba K, Minamino T

Commun Biol (2025) 8 pp. 61-61 [ DOI: doi:10.1038/s42003-025-07485-2 Pubmed: 39820129 ]

EMD-62211
Download Map
3D View
Structure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring protein FliF with C1 symmetry applied
Release date: Jan. 1, 2025
Resolution: 4.2 Å
EM Method: Single-particle

Kinoshita M, Makino F, Miyata T, Imada K, Namba K, Minamino T

Commun Biol (2025) 8 pp. 61-61 [ DOI: doi:10.1038/s42003-025-07485-2 Pubmed: 39820129 ]

EMD-34106
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3D View
Raw data
EMPIAR-11170
GroEL on EG-grid stored for 3 months after graphene oxidation
Release date: Feb. 22, 2023
Resolution: 2.06 Å
EM Method: Single-particle

Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T

Sci Rep (2023) 13 pp. 2279-2279 [ Pubmed: 36755111 DOI: doi:10.1038/s41598-023-29396-0 ]

EMD-34743
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3D View
Raw data
EMPIAR-11304
GroEL on Quantifoil grid
Release date: Feb. 22, 2023
Resolution: 2.81 Å
EM Method: Single-particle

Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T

Sci Rep (2023) 13 pp. 2279-2279 [ Pubmed: 36755111 DOI: doi:10.1038/s41598-023-29396-0 ]

EMD-32159
Download Map
3D View
Raw data
EMPIAR-10954
GroEL on hydrophilized graphene grid high particle density
Release date: Nov. 16, 2022
Resolution: 2.09 Å
EM Method: Single-particle

Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T

Sci Rep (2023) 13 pp. 2279-2279 [ Pubmed: 36755111 DOI: doi:10.1038/s41598-023-29396-0 ]

EMD-32160
Download Map
3D View
Raw data
EMPIAR-10951
SARS-CoV-2 spike protein 1-up RBD on EG-grid
Release date: Nov. 16, 2022
Resolution: 3.1 Å
EM Method: Single-particle

Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T

Sci Rep (2023) 13 pp. 2279-2279 [ Pubmed: 36755111 DOI: doi:10.1038/s41598-023-29396-0 ]

Sort by: Download
Showing 1 - 10 of 26. Page 1 of 3
Display:
Statistics
×

Download











































Preview first 10
Download

Filter By

Current Database

  • EMDB [26]

Current status

  • REL [26]

Sample type

  • Complex [25]
  • Protein [18]
  • Cellular component [1]
  • DNA [1]

Organism

  • Salmonella enterica [10]
  • Escherichia coli [6]
  • Salmonella enterica [6]
  • Homo sapiens [3]
  • Severe acute respiratory syndrome coronavirus [2]
  • Mus musculus [1]
  • Mycoplasma pneumoniae [1]
  • Thermus thermophilus [1]
  • Thermus thermophilus [1]
  • Synthetic construct [1]
  • Gallus gallus [1]

EM Method

  • Single-particle [26]

Resolution

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

Model molecular weight

  • 100-250 kDa [3]
  • 1-2 MDa [1]
  • 2-5 MDa [3]

Release Date

  • 2025 [6]
  • 2023 [2]
  • 2022 [10]
  • 2021 [6]
  • 2020 [2]

Author by name

  • Namba K [26]
  • Makino F [23]
  • Kato T [19]
  • Imada K [12]
  • Kinoshita M [12]
  • Minamino T [12]
  • Anzai I [11]
  • Asahara H [11]
  • Fujita J [11]
  • Inoue T [11]
  • Kishikawa J [11]
  • Kishikawa JI [11]
  • Kumano S [11]
  • Matsuura Y [11]
  • Miyata T [11]
  • Moriguchi M [11]
  • Kawamoto A [7]
  • Homma M [2]
  • Kojima S [2]
  • Sakuma M [2]
  • Takekawa N [2]
  • Aparicio D [1]
  • Ariyoshi M [1]
  • Bierge P [1]
  • Espasa M [1]
  • Esperalba J [1]
  • Fernandez-huerta M [1]
  • Fita I [1]
  • Frangakis AS [1]
  • Fukagawa T [1]
  • Horvath P [1]
  • Illanes R [1]
  • Jiang H [1]
  • Kenri T [1]
  • Lluch-senar M [1]
  • Martin J [1]
  • Matsumoto U [1]
  • Mazzolini R [1]
  • Miyata M [1]
  • Mori S [1]
  • Perez-luque R [1]
  • Pich OQ [1]
  • Pinyol J [1]
  • Sanfeliu I [1]
  • Scheffer MP [1]
  • Shibayama K [1]
  • Vizarraga D [1]
  • Watanabe R [1]

Author by ORCID

  • Namba K [13]
  • Imada K [12]
  • Anzai I [11]
  • Fujita J [11]
  • Kishikawa JI [11]
  • Minamino T [10]
  • Kinoshita M [9]
  • Makino F [6]
  • Kato T [6]
  • Miyata T [5]
  • Kawamoto A [5]
  • Kojima S [2]
  • Takekawa N [2]
  • Scheffer MP [1]
  • Horvath P [1]
  • Fukagawa T [1]
  • Ariyoshi M [1]
  • Illanes R [1]
  • Fernandez-huerta M [1]
  • Aparicio D [1]
  • Kenri T [1]
  • Vizarraga D [1]
  • Mori S [1]
  • Miyata M [1]
  • Jiang H [1]
  • Frangakis AS [1]
  • Perez-luque R [1]
  • Esperalba J [1]
  • Mazzolini R [1]
  • Pich OQ [1]
  • Espasa M [1]

Journal

  • SCI REP [11]
  • NAT COMMUN [6]
  • COMMUN BIOL [5]
  • MBIO [2]
  • BIORXIV [1]
  • PNAS [1]

Software

  • RELION [23]
  • GCTF [3]
  • WARP [3]
  • CRYOSPARC [1]

Microscope

  • JEOL CRYO ARM 300 [21]
  • FEI TITAN KRIOS [4]
  • JEOL CRYO ARM 200 [1]

Electron Source

  • FIELD EMISSION GUN [26]

Film or detector model

  • GATAN K3 6K X 4K [21]
  • FEI FALCON II 4K X 4K [3]
  • FEI FALCON III 4K X 4K [1]
  • GATAN K2 SUMMIT 4K X 4K [1]

External links

  • UniProt [16]
  • PDBe-Kb [15]
  • AlphaFold DB [13]
  • EMPIAR [11]
  • PDB [7]
  • Complex Portal [6]
  • Pfam [6]
  • Gene Ontology [5]
  • InterPro [5]