Edit your search query here and hit Return to execute it:
author:"Yamada Y"

Filter By

Current Database

  • EMDB [16]
  • EMPIAR [2]

Current status

  • REL [18]

Sample type

  • Protein [10]
  • Cell [6]
  • Complex [6]
  • Ligand [6]
  • Cellular component [3]
  • Sample [1]

Organism

  • Mus musculus [12]
  • Oryctolagus cuniculus [5]
  • Achromobacter cycloclastes [2]
  • Homo sapiens [2]
  • Thermus thermophilus [1]
  • Thermus thermophilus [1]

EM Method

  • Single-particle [6]
  • Tomography [5]
  • Helical reconstruction [4]
  • Subtomogram averaging [1]

Resolution

  • ≥ 2Å and < 3Å [4]
  • ≥ 3Å and < 4Å [3]
  • ≥ 4Å and < 5Å [1]
  • ≥ 6Å and < 8Å [2]
  • ≥ 20Å and < 30Å [1]

Model molecular weight

  • 100-250 kDa [5]
  • 500-1000 kDa [2]

Release Date

  • 2025 [10]
  • 2021 [1]
  • 2020 [6]
  • 2015 [1]

Author by name

  • Yamada Y [18]
  • Biertumpfel C [10]
  • Cada AK [10]
  • Mizuno N [10]
  • Alvarez-brecht P [7]
  • Basnet N [7]
  • Bodakuntla S [7]
  • Martinez-sanchez A [7]
  • Taira K [7]
  • Zhang R [7]
  • Adachi N [4]
  • Fujii T [4]
  • Kawasaki M [4]
  • Kohzuma T [4]
  • Koiwai K [4]
  • Moriya T [4]
  • Namba K [4]
  • Senda T [4]
  • Shinoda A [4]
  • Yamaguchi T [4]
  • Yumoto F [4]
  • Truong TV [3]
  • Vasquez-montes V [3]
  • Ahrens S [1]
  • Hanc P [1]
  • Hattori M [1]
  • Huotari J [1]
  • Iborra S [1]
  • Ito K [1]
  • Iwata S [1]
  • Jin F [1]
  • Kjaer S [1]
  • Kusakizako T [1]
  • Liu K [1]
  • Ma J [1]
  • Maturana AD [1]
  • Nakada-nakura Y [1]
  • Nomura N [1]
  • Nomura Y [1]
  • Nureki O [1]
  • Reis E Sousa C [1]
  • Sancho D [1]
  • Schulz O [1]
  • Su S [1]
  • Sun M [1]
  • Takeda H [1]
  • Tomita A [1]
  • Uemura T [1]
  • Wada M [1]
  • Wang J [1]
  • Way M [1]
  • Yu Y [1]

Author by ORCID

  • Mizuno N [4]
  • Cada AK [4]
  • Fujii T [3]
  • Martinez-sanchez A [3]
  • Biertumpfel C [3]
  • Yamada Y [3]
  • Namba K [3]
  • Zhang R [3]
  • Moriya T [2]
  • Yamada Y [2]
  • Senda T [2]
  • Shinoda A [2]
  • Kawasaki M [2]
  • Adachi N [2]
  • Maturana AD [1]
  • Way M [1]
  • Reis E Sousa C [1]
  • Vasquez-montes V [1]
  • Wada M [1]
  • Hanc P [1]
  • Schulz O [1]
  • Iborra S [1]
  • Ito K [1]
  • Hattori M [1]
  • Nomura N [1]
  • Su S [1]
  • Tomita A [1]
  • Truong TV [1]

Journal

  • NATURE [7]
  • PNAS [3]
  • BIORXIV [2]
  • J STRUCT BIOL [2]
  • NAT COMMUN [2]
  • IMMUNITY [1]
  • PLOS BIOL [1]

Software

  • IMOD [6]
  • RELION [6]
  • CTFPHASEFLIP [5]
  • CRYOSPARC [1]
  • GCTF [1]
  • SPIDER, EMAN [1]

Microscope

  • TFS KRIOS [9]
  • FEI TALOS ARCTICA [2]
  • FEI TITAN KRIOS [2]
  • JEOL CRYO ARM 200 [2]
  • JEOL 3200FSC [1]

Electron Source

  • FIELD EMISSION GUN [16]

Film or detector model

  • GATAN K3 BIOQUANTUM 6K X 4K [7]
  • GATAN K2 SUMMIT 4K X 4K [3]
  • GATAN K3 BIOCONTINUUM 6K X 4K [3]
  • FEI FALCON III 4K X 4K [2]
  • TVIPS TEMCAM-F416 4K X 4K [1]

EMPIAR Experiment type

  • EMDB [2]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [2]

External links

  • AlphaFold DB [9]
  • PDB [7]
  • UniProt [7]
  • PDBe-Kb [6]
  • ChEBI [5]
  • DrugBank [5]
  • Pfam [5]
  • Gene Ontology [4]
  • InterPro [4]
  • ChEMBL [3]
  • Complex Portal [2]
  • EMDB [2]
  • EMPIAR [2]
  • SCOP2 [1]
Sort by: Download
Showing 1 - 10 of 18. Page 1 of 2
Display:
Statistics
×

Download












































Preview first 10
Download
EMD-71751
Download Map
3D View
Cryo-ET reconstruction of a regenerating axon after axotomy showing branching microtubules primary mouse thalamus neuronal explant, control
Release date: Dec. 3, 2025
EM Method: Tomography

Bodakuntla S, Taira K, Yamada Y, Alvarez-Brecht P, Cada AK, Basnet N, Zhang R, Martinez-Sanchez A, Biertumpfel C, Mizuno N

Nature (2025) 648 pp. 477-487 [ Pubmed: 41224993 DOI: doi:10.1038/s41586-025-09654-z ]

EMD-71752
Download Map
3D View
Cryo-ET reconstruction of a regenerating axon after axotomy showing branching microtubules primary mouse thalamus neuronal explant
Release date: Dec. 3, 2025
EM Method: Tomography

Bodakuntla S, Taira K, Yamada Y, Alvarez-Brecht P, Cada AK, Basnet N, Zhang R, Martinez-Sanchez A, Biertumpfel C, Mizuno N

Nature (2025) 648 pp. 477-487 [ Pubmed: 41224993 DOI: doi:10.1038/s41586-025-09654-z ]

EMD-71753
Download Map
3D View
Cryo-ET reconstruction of a regenerating axon after axotomy showing polymerizing microtubules primary mouse thalamus neuronal explant
Release date: Dec. 3, 2025
EM Method: Tomography

Bodakuntla S, Taira K, Yamada Y, Alvarez-Brecht P, Cada AK, Basnet N, Zhang R, Martinez-Sanchez A, Biertumpfel C, Mizuno N

Nature (2025) 648 pp. 477-487 [ Pubmed: 41224993 DOI: doi:10.1038/s41586-025-09654-z ]

EMD-71754
Download Map
3D View
Cryo-ET reconstruction of a regenerating axon 24 h after axotomy primary mouse thalamus neuronal explant
Release date: Dec. 3, 2025
EM Method: Tomography

Bodakuntla S, Taira K, Yamada Y, Alvarez-Brecht P, Cada AK, Basnet N, Zhang R, Martinez-Sanchez A, Biertumpfel C, Mizuno N

Nature (2025) 648 pp. 477-487 [ Pubmed: 41224993 DOI: doi:10.1038/s41586-025-09654-z ]

EMD-71755
Download Map
3D View
Cryo-ET reconstruction of a regenerating axon 24 h after axotomy primary mouse thalamus neuronal explant
Release date: Dec. 3, 2025
EM Method: Tomography

Bodakuntla S, Taira K, Yamada Y, Alvarez-Brecht P, Cada AK, Basnet N, Zhang R, Martinez-Sanchez A, Biertumpfel C, Mizuno N

Nature (2025) 648 pp. 477-487 [ Pubmed: 41224993 DOI: doi:10.1038/s41586-025-09654-z ]

EMD-71840
Download Map
3D View
Cryo-ET subtomogram averaging of a stress fiber from a regenerating axon
Release date: Dec. 3, 2025
Resolution: 27.7 Å
EM Method: Subtomogram averaging

Bodakuntla S, Taira K, Yamada Y, Alvarez-Brecht P, Cada AK, Basnet N, Zhang R, Martinez-Sanchez A, Biertumpfel C, Mizuno N

Nature (2025) 648 pp. 477-487 [ Pubmed: 41224993 DOI: doi:10.1038/s41586-025-09654-z ]

EMD-71750
Download Map
3D View
In situ microtubule of EpoB-induced regenerating axons
Release date: Nov. 12, 2025
Resolution: 3.19 Å
EM Method: Helical reconstruction
Fitted PDBs: 9pnd
Q-score: 0.479

Bodakuntla S, Taira K, Yamada Y, Alvarez-Brecht P, Cada AK, Basnet N, Zhang R, Martinez-Sanchez A, Biertumpfel C, Mizuno N

Nature (2025) 648 pp. 477-487 [ Pubmed: 41224993 DOI: doi:10.1038/s41586-025-09654-z ]

EMD-44013
Download Map
3D View
F-actin-Talin R13-DD complex
Release date: Feb. 12, 2025
Resolution: 2.98 Å
EM Method: Helical reconstruction
Fitted PDBs: 9az6
Q-score: 0.485

Biertumpfel C, Yamada Y, Vasquez-Montes V, Truong TV, Cada AK, Mizuno N

PNAS (2025) 122 pp. e2405922122-e2405922122 [ DOI: doi:10.1073/pnas.2405922122 Pubmed: 39903122 ]

EMD-48238
Download Map
3D View
F-actin-Talin R13-DD complex, half-decorated
Release date: Feb. 12, 2025
Resolution: 2.97 Å
EM Method: Helical reconstruction

Biertumpfel C, Yamada Y, Vasquez-Montes V, Truong TV, Cada AK, Mizuno N

PNAS (2025) 122 pp. e2405922122-e2405922122 [ DOI: doi:10.1073/pnas.2405922122 Pubmed: 39903122 ]

EMD-48243
Download Map
3D View
F-actin-Talin R13-DD complex, single-decorated
Release date: Feb. 12, 2025
Resolution: 3.06 Å
EM Method: Helical reconstruction

Biertumpfel C, Yamada Y, Vasquez-Montes V, Truong TV, Cada AK, Mizuno N

PNAS (2025) 122 pp. e2405922122-e2405922122 [ DOI: doi:10.1073/pnas.2405922122 Pubmed: 39903122 ]

Sort by: Download
Showing 1 - 10 of 18. Page 1 of 2
Display:
Statistics
×

Download












































Preview first 10
Download

Filter By

Current Database

  • EMDB [16]
  • EMPIAR [2]

Current status

  • REL [18]

Sample type

  • Protein [10]
  • Cell [6]
  • Complex [6]
  • Ligand [6]
  • Cellular component [3]
  • Sample [1]

Organism

  • Mus musculus [12]
  • Oryctolagus cuniculus [5]
  • Achromobacter cycloclastes [2]
  • Homo sapiens [2]
  • Thermus thermophilus [1]
  • Thermus thermophilus [1]

EM Method

  • Single-particle [6]
  • Tomography [5]
  • Helical reconstruction [4]
  • Subtomogram averaging [1]

Resolution

  • ≥ 2Å and < 3Å [4]
  • ≥ 3Å and < 4Å [3]
  • ≥ 4Å and < 5Å [1]
  • ≥ 6Å and < 8Å [2]
  • ≥ 20Å and < 30Å [1]

Model molecular weight

  • 100-250 kDa [5]
  • 500-1000 kDa [2]

Release Date

  • 2025 [10]
  • 2021 [1]
  • 2020 [6]
  • 2015 [1]

Author by name

  • Yamada Y [18]
  • Biertumpfel C [10]
  • Cada AK [10]
  • Mizuno N [10]
  • Alvarez-brecht P [7]
  • Basnet N [7]
  • Bodakuntla S [7]
  • Martinez-sanchez A [7]
  • Taira K [7]
  • Zhang R [7]
  • Adachi N [4]
  • Fujii T [4]
  • Kawasaki M [4]
  • Kohzuma T [4]
  • Koiwai K [4]
  • Moriya T [4]
  • Namba K [4]
  • Senda T [4]
  • Shinoda A [4]
  • Yamaguchi T [4]
  • Yumoto F [4]
  • Truong TV [3]
  • Vasquez-montes V [3]
  • Ahrens S [1]
  • Hanc P [1]
  • Hattori M [1]
  • Huotari J [1]
  • Iborra S [1]
  • Ito K [1]
  • Iwata S [1]
  • Jin F [1]
  • Kjaer S [1]
  • Kusakizako T [1]
  • Liu K [1]
  • Ma J [1]
  • Maturana AD [1]
  • Nakada-nakura Y [1]
  • Nomura N [1]
  • Nomura Y [1]
  • Nureki O [1]
  • Reis E Sousa C [1]
  • Sancho D [1]
  • Schulz O [1]
  • Su S [1]
  • Sun M [1]
  • Takeda H [1]
  • Tomita A [1]
  • Uemura T [1]
  • Wada M [1]
  • Wang J [1]
  • Way M [1]
  • Yu Y [1]

Author by ORCID

  • Mizuno N [4]
  • Cada AK [4]
  • Fujii T [3]
  • Martinez-sanchez A [3]
  • Biertumpfel C [3]
  • Yamada Y [3]
  • Namba K [3]
  • Zhang R [3]
  • Moriya T [2]
  • Yamada Y [2]
  • Senda T [2]
  • Shinoda A [2]
  • Kawasaki M [2]
  • Adachi N [2]
  • Maturana AD [1]
  • Way M [1]
  • Reis E Sousa C [1]
  • Vasquez-montes V [1]
  • Wada M [1]
  • Hanc P [1]
  • Schulz O [1]
  • Iborra S [1]
  • Ito K [1]
  • Hattori M [1]
  • Nomura N [1]
  • Su S [1]
  • Tomita A [1]
  • Truong TV [1]

Journal

  • NATURE [7]
  • PNAS [3]
  • BIORXIV [2]
  • J STRUCT BIOL [2]
  • NAT COMMUN [2]
  • IMMUNITY [1]
  • PLOS BIOL [1]

Software

  • IMOD [6]
  • RELION [6]
  • CTFPHASEFLIP [5]
  • CRYOSPARC [1]
  • GCTF [1]
  • SPIDER, EMAN [1]

Microscope

  • TFS KRIOS [9]
  • FEI TALOS ARCTICA [2]
  • FEI TITAN KRIOS [2]
  • JEOL CRYO ARM 200 [2]
  • JEOL 3200FSC [1]

Electron Source

  • FIELD EMISSION GUN [16]

Film or detector model

  • GATAN K3 BIOQUANTUM 6K X 4K [7]
  • GATAN K2 SUMMIT 4K X 4K [3]
  • GATAN K3 BIOCONTINUUM 6K X 4K [3]
  • FEI FALCON III 4K X 4K [2]
  • TVIPS TEMCAM-F416 4K X 4K [1]

EMPIAR Experiment type

  • EMDB [2]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [2]

External links

  • AlphaFold DB [9]
  • PDB [7]
  • UniProt [7]
  • PDBe-Kb [6]
  • ChEBI [5]
  • DrugBank [5]
  • Pfam [5]
  • Gene Ontology [4]
  • InterPro [4]
  • ChEMBL [3]
  • Complex Portal [2]
  • EMDB [2]
  • EMPIAR [2]
  • SCOP2 [1]