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author:"Miyata M"

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Current Database

  • EMDB [21]
  • EMPIAR [2]

Current status

  • REL [23]

Sample type

  • Complex [11]
  • Protein [10]
  • Cell [8]
  • Ligand [4]
  • Cellular component [2]

Organism

  • (no species) [7]
  • Neisseria meningitidis [5]
  • Mycoplasma pneumoniae [3]
  • Thermosynechococcus elongatus [2]
  • Thermostichus vulcanus [2]
  • Mycoplasma mobile [2]
  • Mus musculus [1]
  • Candidatus heimdallarchaeota archaeon [1]
  • [mycoplasma] mobile [1]
  • (no species) [1]

EM Method

  • Single-particle [12]
  • Tomography [8]
  • Subtomogram averaging [1]

Resolution

  • ≥ 2Å and < 3Å [5]
  • ≥ 3Å and < 4Å [4]
  • ≥ 4Å and < 5Å [1]
  • ≥ 12Å and < 16Å [1]
  • ≥ 16Å and < 20Å [1]
  • ≥ 20Å and < 30Å [1]

Model molecular weight

  • 50-100 kDa [1]
  • 100-250 kDa [2]
  • 250-500 kDa [1]
  • 500-1000 kDa [1]
  • 1-2 MDa [3]

Release Date

  • 2026 [6]
  • 2025 [11]
  • 2022 [2]
  • 2021 [1]
  • 2020 [3]

Author by name

  • Miyata M [22]
  • Tahara YO [10]
  • Hirakata Y [8]
  • Ikuta T [8]
  • Imachi H [8]
  • Isaji Y [8]
  • Ishii S [8]
  • Kawamoto A [8]
  • Miyazaki M [8]
  • Morono Y [8]
  • Murata K [8]
  • Nakagawa S [8]
  • Nobu MK [8]
  • Ogawara M [8]
  • Okada S [8]
  • Saito Y [8]
  • Sakai S [8]
  • Shimamura S [8]
  • Takai K [8]
  • Takaki Y [8]
  • Takano Y [8]
  • Tasumi E [8]
  • Yoshimura T [8]
  • Namba K [7]
  • Uematsu K [7]
  • Kayama Y [6]
  • Bonomi M [5]
  • Chamot-rooke J [5]
  • Deist P [5]
  • Dumenil G [5]
  • Fernandez-martinez D [5]
  • Goussard S [5]
  • Kato T [5]
  • Morozova T [5]
  • Nishiguchi D [5]
  • Nouchikian L [5]
  • Aparicio D [4]
  • England P [4]
  • Fita I [4]
  • Hamaguchi T [4]
  • Kenri T [4]
  • Miyata T [4]
  • Pinyol J [4]
  • Toyonaga T [4]
  • Vizarraga D [4]
  • Kawakami K [3]
  • Martin J [3]
  • Pich OQ [3]
  • Bierge P [2]
  • Espasa M [2]
  • Esperalba J [2]
  • Frangakis AS [2]
  • Hashiguchi H [2]
  • Hirose Y [2]
  • Hosogi N [2]
  • Illanes R [2]
  • Kamiya N [2]
  • Kosumi D [2]
  • Lluch-senar M [2]
  • Makino F [2]
  • Marcos E [2]
  • Marcos-silva M [2]
  • Matsumoto U [2]
  • Mazzolini R [2]
  • Mori S [2]
  • Narita A [2]
  • Pinol J [2]
  • Sanfeliu I [2]
  • Scheffer MP [2]
  • Shibayama K [2]
  • Yonekura K [2]
  • Ando T [1]
  • Boneca I [1]
  • Fernandez-huerta M [1]
  • Fernández-huerta M [1]
  • Fujita J [1]
  • Kodera N [1]
  • Martín J [1]
  • Nakane D [1]
  • Nishikawa MS [1]
  • Perez-luque R [1]
  • Pérez-luque R [1]
  • Rey M [1]
  • Roel J [1]
  • Roel-touris J [1]
  • Uemtatsu K [1]

Author by ORCID

  • Imachi H [8]
  • Murata K [7]
  • Miyata M [5]
  • Hamaguchi T [3]
  • Yonekura K [2]
  • Kosumi D [2]
  • Kenri T [2]
  • Kawamoto A [2]
  • Kato T [2]
  • Namba K [2]
  • Okada S [1]
  • Miyazaki M [1]
  • Hosogi N [1]
  • Uematsu K [1]
  • Morono Y [1]
  • Nobu MK [1]
  • Ishii S [1]
  • Takaki Y [1]
  • Kawakami K [1]
  • Illanes R [1]
  • Aparicio D [1]
  • Toyonaga T [1]
  • Tahara YO [1]
  • Hashiguchi H [1]
  • Vizarraga D [1]
  • Isaji Y [1]
  • Mori S [1]
  • Miyata T [1]
  • Shimamura S [1]
  • Frangakis AS [1]
  • Pinol J [1]
  • Nakagawa S [1]
  • Yoshimura T [1]
  • Takano Y [1]
  • Fujita J [1]
  • Narita A [1]
  • Ikuta T [1]
  • Pich OQ [1]
  • Takai K [1]

Journal

  • BIORXIV [8]
  • TO BE PUBLISHED [6]
  • NAT COMMUN [4]
  • MBIO [2]
  • SCI ADV [2]
  • PLOS PATHOG [1]

Software

  • IMOD [8]
  • CRYOSPARC [6]
  • RELION [5]
  • COOT [1]

Microscope

  • TFS KRIOS [11]
  • JEOL CRYO ARM 300 [6]
  • FEI TITAN KRIOS [2]
  • JEOL 1010 [1]
  • TFS GLACIOS [1]

Electron Source

  • FIELD EMISSION GUN [20]
  • TUNGSTEN HAIRPIN [1]

Film or detector model

  • FEI FALCON IV 4K X 4K [12]
  • GATAN K3 6K X 4K [4]
  • GATAN K2 SUMMIT 4K X 4K [2]
  • FEI FALCON II 4K X 4K [1]
  • FEI FALCON III 4K X 4K [1]
  • OTHER [1]

EMPIAR Experiment type

  • EMDB [2]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [2]

External links

  • PDB [9]
  • AlphaFold DB [8]
  • UniProt [8]
  • InterPro [5]
  • PDBe-Kb [5]
  • Pfam [5]
  • Gene Ontology [4]
  • ChEBI [2]
  • ChEMBL [2]
  • DrugBank [2]
  • EMDB [2]
  • EMPIAR [2]
Sort by: Download
Showing 1 - 10 of 23. Page 1 of 3
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EMD-55084
Download Map
3D View
Native N.meningitidis PorB bound to the N-terminal domain of rmpM
CryoEM
Release date: Sept. 30, 2026
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 9spg
Q-score: 0.536
Similar entry percentile: 91%

Fernandez-Martinez D, Deist P, Morozova T, Nouchikian L, Goussard S, Nishiguchi D, Rey M, Boneca I, Tahara YO, Miyata M, Bonomi M, Chamot-Rooke J, Dumenil G

To Be Published

EMD-54884
Download Map
3D View
Native Neisseria meninigitidis PilQ, Gate Domain focused map
CryoEM
Focused map
Release date: Sept. 2, 2026
Resolution: 3.3 Å
EM Method: Single-particle

Fernandez-Martinez D, Nouchikian L, Goussard S, Deist P, Morozova T, Nishiguchi D, Miyata M, England P, Bonomi M, Chamot-Rooke J, Dumenil G

To Be Published

EMD-54885
Download Map
3D View
Native Neisseria meningitidis PilQ, N0-domain focused map
CryoEM
Focused map
Release date: Sept. 2, 2026
Resolution: 2.6 Å
EM Method: Single-particle

Fernandez-Martinez D, Nouchikian L, Goussard S, Deist P, Morozova T, Nishiguchi D, Miyata M, England P, Bonomi M, Chamot-Rooke J, Dumenil G

To Be Published

EMD-54886
Download Map
3D View
Neisseria meningitidis Native PilQ protomer, composite map
Composite map
CryoEM
Release date: Sept. 2, 2026
Resolution: 2.14 Å
EM Method: Single-particle
Fitted PDBs: 9sh1
Q-score: 0.45
Similar entry percentile: 5%

Fernandez-Martinez D, Nouchikian L, Goussard S, Deist P, Morozova T, Nishiguchi D, Miyata M, England P, Bonomi M, Chamot-Rooke J, Dumenil G

To Be Published

EMD-54887
Download Map
3D View
Neisseria meningitidis Native PilQ tetradecamer
CryoEM
Consensus map
Release date: Sept. 2, 2026
Resolution: 2.14 Å
EM Method: Single-particle
Fitted PDBs: 9sh2
Q-score: 0.405
Similar entry percentile: 3%

Fernandez-Martinez D, Nouchikian L, Goussard S, Deist P, Morozova T, Nishiguchi D, Miyata M, England P, Bonomi M, Chamot-Rooke J, Dumenil G

To Be Published

EMD-65855
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3D View
In situ subtomogram average of Hodarchaeales HC1 actin filament
CryoEM
Release date: June 24, 2026
Resolution: 19.8 Å
EM Method: Subtomogram averaging
Fitted PDBs: 9wc4
Q-score: 0.053
Similar entry percentile: 75%

Imachi H, Nobu MK, Ishii S, Hashiguchi H, Hirakata Y, Hosogi N, Ikuta T, Isaji Y, Miyata M, Miyazaki M, Morono Y, Murata K, Nakagawa S, Narita A, Ogawara M, Okada S, Saito Y, Sakai S, Shimamura S, Tahara YO, Takaki Y, Takano Y, Tasumi E, Uematsu K, Yoshimura T, Takai K

To Be Published

EMD-64894
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3D View
Tomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell
CryoEM
Release date: June 25, 2025
EM Method: Tomography

Imachi H, Nobu MK, Ishii S, Hirakata Y, Hashiguchi H, Hosogi N, Ikuta T, Isaji Y, Miyata M, Miyazaki M, Morono Y, Murata K, Nakagawa S, Narita A, Ogawara M, Okada S, Saito Y, Sakai S, Shimamura S, Tahara YO, Takaki Y, Takano Y, Tasumi E, Uemtatsu K, Yoshimura T, Takai K

bioRxiv (2025) [ ]

EMPIAR-12411
Related EMDB
EMD-60718
Cryo-EM structure of F1-like ATPase for the gliding motility of Mycoplasma
Release date: June 19, 2025
Dataset size: 1.6 TB
Experiment type: EMDB

Toyonaga T, Kato T, Kawamoto A, Miyata T, Kawakami K, Fujita J, Hamaguchi T, Namba K, Miyata M

Sci Adv (2025) 11 [ DOI: 10.1126/sciadv.adr9319 Pubmed: 40009674 ]

Image sets:
  • Unaligned multi-frame micrographs of Mycoplasma F1-like ATPase
EMD-60718
Download Map
3D View
Raw data
EMPIAR-12411
Cryo-EM structure of G1-ATPase dimer from Mycoplasma mobile gliding machinery
CryoEM
Release date: March 12, 2025
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9io5

Toyonaga T, Kato T, Kawamoto A, Miyata T, Kawakami K, Fujita J, Hamaguchi T, Namba K, Miyata M

Sci Adv (2025) 11 pp. eadr9319-eadr9319 [ DOI: doi:10.1126/sciadv.adr9319 Pubmed: 40009674 ]

EMD-63267
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3D View
Tomogram of a Candidatus Flexarchaeum multiprotrusionis strain SC1 cell
CryoEM
Release date: March 12, 2025
EM Method: Tomography

Imachi H, Nobu MK, Ishii S, Hirakata Y, Ikuta T, Isaji Y, Miyata M, Miyazaki M, Morono Y, Murata K, Nakagawa S, Ogawara M, Okada S, Saito Y, Sakai S, Shimamura S, Tahara YO, Takaki Y, Takano Y, Tasumi E, Uematsu K, Yoshimura T, Takai K

bioRxiv (2025) [ DOI: doi:10.1101/2025.02.26.640444 ]

Sort by: Download
Showing 1 - 10 of 23. Page 1 of 3
Display:
Statistics
×

Download



Preview 10 entries View All Download file

Filter By

Current Database

  • EMDB [21]
  • EMPIAR [2]

Current status

  • REL [23]

Sample type

  • Complex [11]
  • Protein [10]
  • Cell [8]
  • Ligand [4]
  • Cellular component [2]

Organism

  • (no species) [7]
  • Neisseria meningitidis [5]
  • Mycoplasma pneumoniae [3]
  • Thermosynechococcus elongatus [2]
  • Thermostichus vulcanus [2]
  • Mycoplasma mobile [2]
  • Mus musculus [1]
  • Candidatus heimdallarchaeota archaeon [1]
  • [mycoplasma] mobile [1]
  • (no species) [1]

EM Method

  • Single-particle [12]
  • Tomography [8]
  • Subtomogram averaging [1]

Resolution

  • ≥ 2Å and < 3Å [5]
  • ≥ 3Å and < 4Å [4]
  • ≥ 4Å and < 5Å [1]
  • ≥ 12Å and < 16Å [1]
  • ≥ 16Å and < 20Å [1]
  • ≥ 20Å and < 30Å [1]

Model molecular weight

  • 50-100 kDa [1]
  • 100-250 kDa [2]
  • 250-500 kDa [1]
  • 500-1000 kDa [1]
  • 1-2 MDa [3]

Release Date

  • 2026 [6]
  • 2025 [11]
  • 2022 [2]
  • 2021 [1]
  • 2020 [3]

Author by name

  • Miyata M [22]
  • Tahara YO [10]
  • Hirakata Y [8]
  • Ikuta T [8]
  • Imachi H [8]
  • Isaji Y [8]
  • Ishii S [8]
  • Kawamoto A [8]
  • Miyazaki M [8]
  • Morono Y [8]
  • Murata K [8]
  • Nakagawa S [8]
  • Nobu MK [8]
  • Ogawara M [8]
  • Okada S [8]
  • Saito Y [8]
  • Sakai S [8]
  • Shimamura S [8]
  • Takai K [8]
  • Takaki Y [8]
  • Takano Y [8]
  • Tasumi E [8]
  • Yoshimura T [8]
  • Namba K [7]
  • Uematsu K [7]
  • Kayama Y [6]
  • Bonomi M [5]
  • Chamot-rooke J [5]
  • Deist P [5]
  • Dumenil G [5]
  • Fernandez-martinez D [5]
  • Goussard S [5]
  • Kato T [5]
  • Morozova T [5]
  • Nishiguchi D [5]
  • Nouchikian L [5]
  • Aparicio D [4]
  • England P [4]
  • Fita I [4]
  • Hamaguchi T [4]
  • Kenri T [4]
  • Miyata T [4]
  • Pinyol J [4]
  • Toyonaga T [4]
  • Vizarraga D [4]
  • Kawakami K [3]
  • Martin J [3]
  • Pich OQ [3]
  • Bierge P [2]
  • Espasa M [2]
  • Esperalba J [2]
  • Frangakis AS [2]
  • Hashiguchi H [2]
  • Hirose Y [2]
  • Hosogi N [2]
  • Illanes R [2]
  • Kamiya N [2]
  • Kosumi D [2]
  • Lluch-senar M [2]
  • Makino F [2]
  • Marcos E [2]
  • Marcos-silva M [2]
  • Matsumoto U [2]
  • Mazzolini R [2]
  • Mori S [2]
  • Narita A [2]
  • Pinol J [2]
  • Sanfeliu I [2]
  • Scheffer MP [2]
  • Shibayama K [2]
  • Yonekura K [2]
  • Ando T [1]
  • Boneca I [1]
  • Fernandez-huerta M [1]
  • Fernández-huerta M [1]
  • Fujita J [1]
  • Kodera N [1]
  • Martín J [1]
  • Nakane D [1]
  • Nishikawa MS [1]
  • Perez-luque R [1]
  • Pérez-luque R [1]
  • Rey M [1]
  • Roel J [1]
  • Roel-touris J [1]
  • Uemtatsu K [1]

Author by ORCID

  • Imachi H [8]
  • Murata K [7]
  • Miyata M [5]
  • Hamaguchi T [3]
  • Yonekura K [2]
  • Kosumi D [2]
  • Kenri T [2]
  • Kawamoto A [2]
  • Kato T [2]
  • Namba K [2]
  • Okada S [1]
  • Miyazaki M [1]
  • Hosogi N [1]
  • Uematsu K [1]
  • Morono Y [1]
  • Nobu MK [1]
  • Ishii S [1]
  • Takaki Y [1]
  • Kawakami K [1]
  • Illanes R [1]
  • Aparicio D [1]
  • Toyonaga T [1]
  • Tahara YO [1]
  • Hashiguchi H [1]
  • Vizarraga D [1]
  • Isaji Y [1]
  • Mori S [1]
  • Miyata T [1]
  • Shimamura S [1]
  • Frangakis AS [1]
  • Pinol J [1]
  • Nakagawa S [1]
  • Yoshimura T [1]
  • Takano Y [1]
  • Fujita J [1]
  • Narita A [1]
  • Ikuta T [1]
  • Pich OQ [1]
  • Takai K [1]

Journal

  • BIORXIV [8]
  • TO BE PUBLISHED [6]
  • NAT COMMUN [4]
  • MBIO [2]
  • SCI ADV [2]
  • PLOS PATHOG [1]

Software

  • IMOD [8]
  • CRYOSPARC [6]
  • RELION [5]
  • COOT [1]

Microscope

  • TFS KRIOS [11]
  • JEOL CRYO ARM 300 [6]
  • FEI TITAN KRIOS [2]
  • JEOL 1010 [1]
  • TFS GLACIOS [1]

Electron Source

  • FIELD EMISSION GUN [20]
  • TUNGSTEN HAIRPIN [1]

Film or detector model

  • FEI FALCON IV 4K X 4K [12]
  • GATAN K3 6K X 4K [4]
  • GATAN K2 SUMMIT 4K X 4K [2]
  • FEI FALCON II 4K X 4K [1]
  • FEI FALCON III 4K X 4K [1]
  • OTHER [1]

EMPIAR Experiment type

  • EMDB [2]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [2]

External links

  • PDB [9]
  • AlphaFold DB [8]
  • UniProt [8]
  • InterPro [5]
  • PDBe-Kb [5]
  • Pfam [5]
  • Gene Ontology [4]
  • ChEBI [2]
  • ChEMBL [2]
  • DrugBank [2]
  • EMDB [2]
  • EMPIAR [2]