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:"JP17pc0101020"

Filter By

Current Database

  • EMDB [38]

Current status

  • REL [38]

Sample type

  • Complex [37]
  • Protein [33]
  • Ligand [5]
  • Cellular component [1]
  • DNA [1]

Organism

  • Severe acute respiratory syndrome coronavirus [12]
  • Salmonella enterica [7]
  • Homo sapiens [7]
  • Escherichia coli [6]
  • Salmonella enterica [6]
  • Mus musculus [4]
  • Vicugna pacos [4]
  • Klebsiella pneumoniae [3]
  • Klebsiella pneumoniae [1]
  • Mycoplasma pneumoniae [1]
  • Ureaplasma parvum [1]
  • Thermus thermophilus [1]
  • Thermus thermophilus [1]
  • Synthetic construct [1]
  • Klebsiella pneumoniae [1]
  • Escherichia coli [1]
  • Gallus gallus [1]

EM Method

  • Single-particle [35]
  • Helical reconstruction [3]

Resolution

  • < 2Å [3]
  • ≥ 2Å and < 3Å [14]
  • ≥ 3Å and < 4Å [17]
  • ≥ 4Å and < 5Å [1]
  • ≥ 6Å and < 8Å [2]
  • ≥ 8Å and < 12Å [1]

Model molecular weight

  • 100-250 kDa [5]
  • 250-500 kDa [3]
  • 1-2 MDa [1]
  • 2-5 MDa [3]
  • 5-10 MDa [1]

Release Date

  • 2025 [8]
  • 2023 [9]
  • 2022 [16]
  • 2021 [3]
  • 2020 [2]

Author by name

  • Namba K [38]
  • Makino F [28]
  • Fujita J [26]
  • Inoue T [22]
  • Anzai I [21]
  • Matsuura Y [21]
  • Kato T [17]
  • Asahara H [11]
  • Kishikawa J [11]
  • Kishikawa JI [11]
  • Kumano S [11]
  • Moriguchi M [11]
  • Imada K [9]
  • Kinoshita M [9]
  • Minamino T [9]
  • Miyata T [9]
  • Watanabe T [8]
  • Kasai K [5]
  • Suzuki K [5]
  • Imura A [4]
  • Kajita T [4]
  • Kawamoto A [4]
  • Kazuma Y [4]
  • Konishi Y [4]
  • Kosaka Y [4]
  • Maeda R [4]
  • Miyakawa K [4]
  • Miyamoto Y [4]
  • Nagata K [4]
  • Ono C [4]
  • Ryo A [4]
  • Sato K [4]
  • Shichinohe S [4]
  • Shirakawa K [4]
  • Taguwa S [4]
  • Takada K [4]
  • Takaori-kondo A [4]
  • Torii S [4]
  • Yamaguchi K [4]
  • Yamaoka Y [4]
  • Yamazaki H [4]
  • Hibino K [3]
  • Kamimura N [3]
  • Kato Y [3]
  • Matsumura H [3]
  • Tsumoto K [3]
  • Amesaka H [2]
  • Aoyama H [2]
  • Hara M [2]
  • Homma M [2]
  • Imadome K [2]
  • Imadome KI [2]
  • Ishii KJ [2]
  • Ito T [2]
  • Kamitani W [2]
  • Kobiyama K [2]
  • Kojima S [2]
  • Konishi T [2]
  • Kuroda N [2]
  • Minamitani T [2]
  • Otsubo R [2]
  • Sakuma M [2]
  • Takekawa N [2]
  • Tanaka S [2]
  • Tanaka SI [2]
  • Tanino H [2]
  • Ueno S [2]
  • Yasui T [2]
  • Yoshizawa T [2]
  • Akiba H [1]
  • Aparicio D [1]
  • Ariyoshi M [1]
  • Bierge P [1]
  • Ekimoto T [1]
  • Espasa M [1]
  • Esperalba J [1]
  • Fernandez-huerta M [1]
  • Fita I [1]
  • Frangakis AS [1]
  • Fukagawa T [1]
  • Fukuda Y [1]
  • Harada K [1]
  • Horvath P [1]
  • Ikeguchi M [1]
  • Illanes R [1]
  • Inoue M [1]
  • Ise T [1]
  • Jiang H [1]
  • Kagoshima G [1]
  • Kamada H [1]
  • Kenri T [1]
  • Lluch-senar M [1]
  • Martin J [1]
  • Matsumoto U [1]
  • Mazzolini R [1]
  • Miyata M [1]
  • Mori S [1]
  • Nagata S [1]
  • Nakura Y [1]
  • Nishiyama K [1]

Author by ORCID

  • Fujita J [25]
  • Namba K [22]
  • Anzai I [21]
  • Makino F [11]
  • Kishikawa JI [11]
  • Imada K [9]
  • Matsuura Y [8]
  • Minamino T [7]
  • Inoue T [6]
  • Kinoshita M [6]
  • Kasai K [5]
  • Ryo A [4]
  • Takaori-kondo A [4]
  • Yamaoka Y [4]
  • Kazuma Y [4]
  • Maeda R [4]
  • Miyakawa K [4]
  • Yamaguchi K [4]
  • Shirakawa K [4]
  • Yamazaki H [4]
  • Watanabe T [4]
  • Imura A [4]
  • Kato T [4]
  • Konishi Y [4]
  • Sato K [4]
  • Miyata T [3]
  • Matsumura H [3]
  • Aoyama H [2]
  • Kojima S [2]
  • Kawamoto A [2]
  • Amesaka H [2]
  • Takekawa N [2]
  • Tanaka SI [2]
  • Scheffer MP [1]
  • Horvath P [1]
  • Tsumoto K [1]
  • Fukagawa T [1]
  • Ise T [1]
  • Nagata S [1]
  • Uchihashi T [1]
  • Ariyoshi M [1]
  • Akiba H [1]
  • Illanes R [1]
  • Fernandez-huerta M [1]
  • Aparicio D [1]
  • Nishiyama K [1]
  • Kamada H [1]
  • Kenri T [1]
  • Ohno H [1]
  • Vizarraga D [1]
  • Mori S [1]
  • Fukuda Y [1]
  • Miyata M [1]
  • Jiang H [1]
  • Frangakis AS [1]
  • Harada K [1]
  • Perez-luque R [1]
  • Esperalba J [1]
  • Mazzolini R [1]
  • Pich OQ [1]
  • Espasa M [1]
  • Tobita S [1]

Journal

  • SCI REP [13]
  • COMMUN BIOL [10]
  • NAT COMMUN [6]
  • TO BE PUBLISHED [4]
  • MBIO [2]
  • BIORXIV [1]
  • J MOL BIOL [1]
  • PNAS [1]

Software

  • RELION [30]
  • CRYOSPARC [10]
  • GCTF [3]

Microscope

  • JEOL CRYO ARM 300 [33]
  • FEI TITAN KRIOS [4]
  • JEOL CRYO ARM 200 [1]

Electron Source

  • FIELD EMISSION GUN [38]

Film or detector model

  • GATAN K3 6K X 4K [33]
  • FEI FALCON II 4K X 4K [3]
  • FEI FALCON III 4K X 4K [1]
  • GATAN K2 SUMMIT 4K X 4K [1]

External links

  • UniProt [31]
  • PDBe-Kb [28]
  • AlphaFold DB [18]
  • Complex Portal [16]
  • EMPIAR [13]
  • PDB [13]
  • Pfam [12]
  • Gene Ontology [11]
  • InterPro [9]
  • ChEBI [5]
  • ChEMBL [5]
  • DrugBank [4]
Sort by: Download
Showing 1 - 10 of 38. Page 1 of 4
Display:
Statistics
×

Download











































Preview first 10
Download
EMD-60854
Download Map
3D View
Cryo-EM structure of urease from Ureaplasma parvum
Release date: Aug. 20, 2025
Resolution: 2.03 Å
EM Method: Single-particle
Fitted PDBs: 9it2

Wu HN, Fujita J, Nakura Y, Inoue M, Suzuki K, Ekimoto T, Yin B, Fukuda Y, Harada K, Inoue T, Ikeguchi M, Namba K, Yanagihara I

J Mol Biol (2025) 437 pp. 169368-169368 [ Pubmed: 40752870 DOI: doi:10.1016/j.jmb.2025.169368 ]

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-60837
Download Map
3D View
Cryo-EM structure of KpFtsZ-ZapA complex
Release date: July 23, 2025
Resolution: 2.73 Å
EM Method: Helical reconstruction
Fitted PDBs: 9isk
Q-score: 0.554

Fujita J, Kasai K, Hibino K, Kagoshima G, Kamimura N, Tobita S, Kato Y, Uehara R, Namba K, Uchihashi T, Matsumura H

Nat Commun (2025) 16 pp. 5985-5985 [ Pubmed: 40593603 DOI: doi:10.1038/s41467-025-60940-w ]

EMD-60007
Download Map
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-34871
Download Map
3D View
Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2
Release date: Oct. 4, 2023
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 8hlb
Q-score: 0.446

Akiba H, Fujita J, Ise T, Nishiyama K, Miyata T, Kato T, Namba K, Ohno H, Kamada H, Nagata S, Tsumoto K

Commun Biol (2023) 6 pp. 987-987 [ Pubmed: 37758868 DOI: doi:10.1038/s42003-023-05326-8 ]

EMD-33972
Download Map
3D View
Cryo-EM structure of the SARS-CoV-2 spike protein 3-up RBD bound to neutralizing antibody CSW1-1805
Release date: Aug. 9, 2023
Resolution: 3.62 Å
EM Method: Single-particle

Anzai I, Fujita J, Ono C, Kosaka Y, Miyamoto Y, Shichinohe S, Takada K, Torii S, Taguwa S, Suzuki K, Makino F, Kajita T, Inoue T, Namba K, Watanabe T, Matsuura Y

To Be Published

Sort by: Download
Showing 1 - 10 of 38. Page 1 of 4
Display:
Statistics
×

Download











































Preview first 10
Download

Filter By

Current Database

  • EMDB [38]

Current status

  • REL [38]

Sample type

  • Complex [37]
  • Protein [33]
  • Ligand [5]
  • Cellular component [1]
  • DNA [1]

Organism

  • Severe acute respiratory syndrome coronavirus [12]
  • Salmonella enterica [7]
  • Homo sapiens [7]
  • Escherichia coli [6]
  • Salmonella enterica [6]
  • Mus musculus [4]
  • Vicugna pacos [4]
  • Klebsiella pneumoniae [3]
  • Klebsiella pneumoniae [1]
  • Mycoplasma pneumoniae [1]
  • Ureaplasma parvum [1]
  • Thermus thermophilus [1]
  • Thermus thermophilus [1]
  • Synthetic construct [1]
  • Klebsiella pneumoniae [1]
  • Escherichia coli [1]
  • Gallus gallus [1]

EM Method

  • Single-particle [35]
  • Helical reconstruction [3]

Resolution

  • < 2Å [3]
  • ≥ 2Å and < 3Å [14]
  • ≥ 3Å and < 4Å [17]
  • ≥ 4Å and < 5Å [1]
  • ≥ 6Å and < 8Å [2]
  • ≥ 8Å and < 12Å [1]

Model molecular weight

  • 100-250 kDa [5]
  • 250-500 kDa [3]
  • 1-2 MDa [1]
  • 2-5 MDa [3]
  • 5-10 MDa [1]

Release Date

  • 2025 [8]
  • 2023 [9]
  • 2022 [16]
  • 2021 [3]
  • 2020 [2]

Author by name

  • Namba K [38]
  • Makino F [28]
  • Fujita J [26]
  • Inoue T [22]
  • Anzai I [21]
  • Matsuura Y [21]
  • Kato T [17]
  • Asahara H [11]
  • Kishikawa J [11]
  • Kishikawa JI [11]
  • Kumano S [11]
  • Moriguchi M [11]
  • Imada K [9]
  • Kinoshita M [9]
  • Minamino T [9]
  • Miyata T [9]
  • Watanabe T [8]
  • Kasai K [5]
  • Suzuki K [5]
  • Imura A [4]
  • Kajita T [4]
  • Kawamoto A [4]
  • Kazuma Y [4]
  • Konishi Y [4]
  • Kosaka Y [4]
  • Maeda R [4]
  • Miyakawa K [4]
  • Miyamoto Y [4]
  • Nagata K [4]
  • Ono C [4]
  • Ryo A [4]
  • Sato K [4]
  • Shichinohe S [4]
  • Shirakawa K [4]
  • Taguwa S [4]
  • Takada K [4]
  • Takaori-kondo A [4]
  • Torii S [4]
  • Yamaguchi K [4]
  • Yamaoka Y [4]
  • Yamazaki H [4]
  • Hibino K [3]
  • Kamimura N [3]
  • Kato Y [3]
  • Matsumura H [3]
  • Tsumoto K [3]
  • Amesaka H [2]
  • Aoyama H [2]
  • Hara M [2]
  • Homma M [2]
  • Imadome K [2]
  • Imadome KI [2]
  • Ishii KJ [2]
  • Ito T [2]
  • Kamitani W [2]
  • Kobiyama K [2]
  • Kojima S [2]
  • Konishi T [2]
  • Kuroda N [2]
  • Minamitani T [2]
  • Otsubo R [2]
  • Sakuma M [2]
  • Takekawa N [2]
  • Tanaka S [2]
  • Tanaka SI [2]
  • Tanino H [2]
  • Ueno S [2]
  • Yasui T [2]
  • Yoshizawa T [2]
  • Akiba H [1]
  • Aparicio D [1]
  • Ariyoshi M [1]
  • Bierge P [1]
  • Ekimoto T [1]
  • Espasa M [1]
  • Esperalba J [1]
  • Fernandez-huerta M [1]
  • Fita I [1]
  • Frangakis AS [1]
  • Fukagawa T [1]
  • Fukuda Y [1]
  • Harada K [1]
  • Horvath P [1]
  • Ikeguchi M [1]
  • Illanes R [1]
  • Inoue M [1]
  • Ise T [1]
  • Jiang H [1]
  • Kagoshima G [1]
  • Kamada H [1]
  • Kenri T [1]
  • Lluch-senar M [1]
  • Martin J [1]
  • Matsumoto U [1]
  • Mazzolini R [1]
  • Miyata M [1]
  • Mori S [1]
  • Nagata S [1]
  • Nakura Y [1]
  • Nishiyama K [1]

Author by ORCID

  • Fujita J [25]
  • Namba K [22]
  • Anzai I [21]
  • Makino F [11]
  • Kishikawa JI [11]
  • Imada K [9]
  • Matsuura Y [8]
  • Minamino T [7]
  • Inoue T [6]
  • Kinoshita M [6]
  • Kasai K [5]
  • Ryo A [4]
  • Takaori-kondo A [4]
  • Yamaoka Y [4]
  • Kazuma Y [4]
  • Maeda R [4]
  • Miyakawa K [4]
  • Yamaguchi K [4]
  • Shirakawa K [4]
  • Yamazaki H [4]
  • Watanabe T [4]
  • Imura A [4]
  • Kato T [4]
  • Konishi Y [4]
  • Sato K [4]
  • Miyata T [3]
  • Matsumura H [3]
  • Aoyama H [2]
  • Kojima S [2]
  • Kawamoto A [2]
  • Amesaka H [2]
  • Takekawa N [2]
  • Tanaka SI [2]
  • Scheffer MP [1]
  • Horvath P [1]
  • Tsumoto K [1]
  • Fukagawa T [1]
  • Ise T [1]
  • Nagata S [1]
  • Uchihashi T [1]
  • Ariyoshi M [1]
  • Akiba H [1]
  • Illanes R [1]
  • Fernandez-huerta M [1]
  • Aparicio D [1]
  • Nishiyama K [1]
  • Kamada H [1]
  • Kenri T [1]
  • Ohno H [1]
  • Vizarraga D [1]
  • Mori S [1]
  • Fukuda Y [1]
  • Miyata M [1]
  • Jiang H [1]
  • Frangakis AS [1]
  • Harada K [1]
  • Perez-luque R [1]
  • Esperalba J [1]
  • Mazzolini R [1]
  • Pich OQ [1]
  • Espasa M [1]
  • Tobita S [1]

Journal

  • SCI REP [13]
  • COMMUN BIOL [10]
  • NAT COMMUN [6]
  • TO BE PUBLISHED [4]
  • MBIO [2]
  • BIORXIV [1]
  • J MOL BIOL [1]
  • PNAS [1]

Software

  • RELION [30]
  • CRYOSPARC [10]
  • GCTF [3]

Microscope

  • JEOL CRYO ARM 300 [33]
  • FEI TITAN KRIOS [4]
  • JEOL CRYO ARM 200 [1]

Electron Source

  • FIELD EMISSION GUN [38]

Film or detector model

  • GATAN K3 6K X 4K [33]
  • FEI FALCON II 4K X 4K [3]
  • FEI FALCON III 4K X 4K [1]
  • GATAN K2 SUMMIT 4K X 4K [1]

External links

  • UniProt [31]
  • PDBe-Kb [28]
  • AlphaFold DB [18]
  • Complex Portal [16]
  • EMPIAR [13]
  • PDB [13]
  • Pfam [12]
  • Gene Ontology [11]
  • InterPro [9]
  • ChEBI [5]
  • ChEMBL [5]
  • DrugBank [4]