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:"JP21am0101118"

Filter By

Current Database

  • EMDB [18]

Current status

  • REL [18]

Sample type

  • Complex [18]
  • Protein [17]
  • Ligand [14]

Organism

  • Rhodospirillum rubrum [4]
  • Halorhodospira halophila [3]
  • Homo sapiens [3]
  • Mus musculus [2]
  • Rhodothalassium salexigens [2]
  • Cereibacter sphaeroides [2]
  • Allochromatium vinosum [2]
  • Rhodobacter capsulatus [1]
  • Cereibacter sphaeroides [1]
  • Rhodopila globiformis [1]
  • Blastochloris tepida [1]
  • Rhodospirillum rubrum [1]
  • Allochromatium tepidum [1]

EM Method

  • Single-particle [18]

Resolution

  • ≥ 2Å and < 3Å [15]
  • ≥ 3Å and < 4Å [2]
  • ≥ 4Å and < 5Å [1]

Model molecular weight

  • 0-50 kDa [1]
  • 100-250 kDa [2]
  • 250-500 kDa [10]
  • 500-1000 kDa [4]

Release Date

  • 2025 [5]
  • 2024 [6]
  • 2023 [1]
  • 2022 [4]
  • 2021 [2]

Author by name

  • Hall M [18]
  • Humbel BM [18]
  • Kanno R [18]
  • Mizoguchi A [18]
  • Tani K [18]
  • Kimura Y [15]
  • Madigan MT [15]
  • Wang-otomo ZY [15]
  • Yu LJ [14]
  • Wang-otomo Z-Y [10]
  • Nagashima KVP [9]
  • Yu L-J [9]
  • Purba ER [8]
  • Takaichi S [6]
  • Ji XC [5]
  • Takenaka S [5]
  • Inoue K [4]
  • Nagashima S [4]
  • Doi T [3]
  • Hamaguchi T [3]
  • Hiwatashi N [3]
  • Ji X-C [3]
  • Kawakami M [3]
  • Kawamura S [3]
  • Kikuchi R [3]
  • Kobayashi Y [3]
  • Maki-yonekura S [3]
  • Minamino A [3]
  • Mochizuki T [3]
  • Nakata K [3]
  • Negami T [3]
  • Terada T [3]
  • Yonekura K [3]
  • Harada A [2]
  • Inada K [2]
  • Inami M [2]
  • Iwasaki K [2]
  • Kobayashi A [2]
  • Matsushita R [2]
  • Nakamura N [2]
  • Ooya T [2]
  • Satoh I [2]
  • Takahashi A [2]
  • Dewa T [1]
  • Honda M [1]
  • Hosogi N [1]
  • Isawa Y [1]
  • Ishikawa I [1]
  • Izumida A [1]
  • Kishikawa J [1]
  • Kishikawa JI [1]
  • Kobayashi K [1]
  • Kojima R [1]
  • Kondo M [1]
  • Kurosawa K [1]
  • Matsuda Y [1]
  • Mino H [1]
  • Mio K [1]
  • Mitsuoka K [1]
  • Mori K [1]
  • Morishita R [1]
  • Nagasawa Y [1]
  • Nagashima VP [1]
  • Ohkubo T [1]
  • Okura Y [1]
  • Sasaki YC [1]
  • Seto R [1]
  • Tsukatani Y [1]

Author by ORCID

  • Tani K [18]
  • Wang-otomo ZY [14]
  • Kimura Y [14]
  • Yu LJ [10]
  • Takaichi S [6]
  • Kanno R [5]
  • Yonekura K [3]
  • Doi T [3]
  • Terada T [3]
  • Humbel BM [3]
  • Maki-yonekura S [3]
  • Hamaguchi T [3]
  • Iwasaki K [2]
  • Hosogi N [1]
  • Nagasawa Y [1]
  • Dewa T [1]
  • Kondo M [1]
  • Kishikawa JI [1]
  • Mino H [1]
  • Nagashima S [1]
  • Kojima R [1]

Journal

  • COMMUN BIOL [8]
  • NAT COMMUN [5]
  • BIOCHEMISTRY [4]
  • J BIOL CHEM [1]

Software

  • RELION [12]
  • CTFFIND [3]

Microscope

  • FEI TITAN KRIOS [9]
  • JEOL CRYO ARM 300 [4]
  • TFS KRIOS [3]
  • FEI TALOS ARCTICA [1]
  • FEI TECNAI ARCTICA [1]

Electron Source

  • FIELD EMISSION GUN [18]

Film or detector model

  • FEI FALCON III 4K X 4K [14]
  • GATAN K3 6K X 4K [4]

External links

  • PDB [17]
  • UniProt [16]
  • AlphaFold DB [14]
  • ChEBI [14]
  • ChEMBL [14]
  • DrugBank [14]
  • Gene Ontology [14]
  • Pfam [14]
  • InterPro [13]
  • PDBe-Kb [13]
  • SCOP2 [1]
Sort by: Download
Showing 1 - 10 of 18. Page 1 of 2
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EMD-63714
Download Map
3D View
Structure of photosynthetic LH1-RC complex the Halophilic Nonsulfur Purple Bacterium, Rhodothalassium salexigens
Release date: July 2, 2025
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 9m8m
Q-score: 0.666

Tani K, Kanno R, Inami M, Ooya T, Matsushita R, Inada K, Takenaka S, Takaichi S, Purba ER, Hall M, Mochizuki T, Yu LJ, Mizoguchi A, Humbel BM, Madigan MT, Kimura Y, Wang-Otomo ZY

Biochemistry (2025) 64 pp. 3070-3080 [ DOI: doi:10.1021/acs.biochem.5c00181 Pubmed: 40551662 ]

EMD-64946
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3D View
Map including micelle density from the photosynthetic LH1-RC complex of the halophilic nonsulfur purple bacterium Rhodothalassium salexigens
Release date: July 2, 2025
Resolution: 2.3 Å
EM Method: Single-particle

Tani K, Kanno R, Inami M, Ooya T, Matsushita R, Inada K, Takenaka S, Takaichi S, Purba ER, Hall M, Mochizuki T, Yu LJ, Mizoguchi A, Humbel BM, Madigan MT, Kimura Y, Wang-Otomo ZY

Biochemistry (2025) 64 pp. 3070-3080 [ DOI: doi:10.1021/acs.biochem.5c00181 Pubmed: 40551662 ]

EMD-39835
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3D View
Photosynthetic LH2-LH1 complex from the purple bacterium Halorhodospira halophila
Release date: Feb. 19, 2025
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8z81
Q-score: 0.682

Tani K, Nagashima KVP, Kojima R, Kondo M, Kanno R, Satoh I, Kawakami M, Hiwatashi N, Nakata K, Nagashima S, Inoue K, Isawa Y, Morishita R, Takaichi S, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Humbel BM, Kimura Y, Nagasawa Y, Dewa T, Wang-Otomo ZY

Nat Commun (2025) 16 pp. 1410-1410 [ DOI: doi:10.1038/s41467-024-55811-9 Pubmed: 39915441 ]

EMD-39836
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3D View
Photosynthetic LH1-RC-HiPIP complex from the purple bacterium Halorhodospira halophila
Release date: Jan. 29, 2025
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8z82
Q-score: 0.639

Tani K, Kanno R, Nagashima KVP, Kawakami M, Hiwatashi N, Nakata K, Nagashima S, Inoue K, Takaichi S, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Humbel BM, Kimura Y, Wang-Otomo ZY

Commun Biol (2025) 8 pp. 42-42 [ DOI: doi:10.1038/s42003-024-07421-w Pubmed: 39799244 ]

EMD-39837
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3D View
Photosynthetic LH1-RC complex from the purple bacterium Halorhodospira halophila
Release date: Jan. 29, 2025
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8z83

Tani K, Kanno R, Nagashima KVP, Kawakami M, Hiwatashi N, Nakata K, Nagashima S, Inoue K, Takaichi S, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Humbel BM, Kimura Y, Wang-Otomo ZY

Commun Biol (2025) 8 pp. 42-42 [ DOI: doi:10.1038/s42003-024-07421-w Pubmed: 39799244 ]

EMD-61095
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3D View
Structure of photosynthetic LH1-RC complex from the purple bacterium Blastochloris tepida
Release date: Dec. 18, 2024
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 9j2f
Q-score: 0.725

Kimura Y, Kanno R, Mori K, Matsuda Y, Seto R, Takenaka S, Mino H, Ohkubo T, Honda M, Sasaki YC, Kishikawa JI, Mitsuoka K, Mio K, Hall M, Purba ER, Mochizuki T, Mizoguchi A, Humbel BM, Madigan MT, Wang-Otomo ZY, Tani K

Biochemistry (2025) 64 pp. 170-179 [ DOI: doi:10.1021/acs.biochem.4c00506 Pubmed: 39680849 ]

EMD-38740
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3D View
Cryo-EM structure of ET-1 bound ETBR-DNGI complex
Release date: Oct. 2, 2024
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 8xwp
Q-score: 0.454

Tani K, Maki-Yonekura S, Kanno R, Negami T, Hamaguchi T, Hall M, Mizoguchi A, Humbel BM, Terada T, Yonekura K, Doi T

Commun Biol (2024) 7 pp. 1303-1303 [ Pubmed: 39414992 DOI: doi:10.1038/s42003-024-06905-z ]

EMD-38741
Download Map
3D View
Cryo-EM structure of ET-1 bound ETBR-DNGI complex
Release date: Oct. 2, 2024
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 8xwq
Q-score: 0.29

Tani K, Maki-Yonekura S, Kanno R, Negami T, Hamaguchi T, Hall M, Mizoguchi A, Humbel BM, Terada T, Yonekura K, Doi T

Commun Biol (2024) 7 pp. 1303-1303 [ Pubmed: 39414992 DOI: doi:10.1038/s42003-024-06905-z ]

EMD-60404
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3D View
Cryo-EM structure focused on the receptor of the ET-1 bound ETBR-DNGI complex
Release date: Oct. 2, 2024
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 8zrt
Q-score: 0.443

Tani K, Maki-Yonekura S, Kanno R, Negami T, Hamaguchi T, Hall M, Mizoguchi A, Humbel BM, Terada T, Yonekura K, Doi T

Commun Biol (2024) 7 pp. 1303-1303 [ Pubmed: 39414992 DOI: doi:10.1038/s42003-024-06905-z ]

EMD-37465
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Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density
Release date: Feb. 21, 2024
Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8wdu
Q-score: 0.676

Tani K, Kanno R, Harada A, Kobayashi Y, Minamino A, Takenaka S, Nakamura N, Ji XC, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Iwasaki K, Humbel BM, Kimura Y, Wang-Otomo ZY

Commun Biol (2024) 7 pp. 176-176 [ Pubmed: 38347078 DOI: doi:10.1038/s42003-024-05863-w ]

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

Download











































Preview first 10
Download

Filter By

Current Database

  • EMDB [18]

Current status

  • REL [18]

Sample type

  • Complex [18]
  • Protein [17]
  • Ligand [14]

Organism

  • Rhodospirillum rubrum [4]
  • Halorhodospira halophila [3]
  • Homo sapiens [3]
  • Mus musculus [2]
  • Rhodothalassium salexigens [2]
  • Cereibacter sphaeroides [2]
  • Allochromatium vinosum [2]
  • Rhodobacter capsulatus [1]
  • Cereibacter sphaeroides [1]
  • Rhodopila globiformis [1]
  • Blastochloris tepida [1]
  • Rhodospirillum rubrum [1]
  • Allochromatium tepidum [1]

EM Method

  • Single-particle [18]

Resolution

  • ≥ 2Å and < 3Å [15]
  • ≥ 3Å and < 4Å [2]
  • ≥ 4Å and < 5Å [1]

Model molecular weight

  • 0-50 kDa [1]
  • 100-250 kDa [2]
  • 250-500 kDa [10]
  • 500-1000 kDa [4]

Release Date

  • 2025 [5]
  • 2024 [6]
  • 2023 [1]
  • 2022 [4]
  • 2021 [2]

Author by name

  • Hall M [18]
  • Humbel BM [18]
  • Kanno R [18]
  • Mizoguchi A [18]
  • Tani K [18]
  • Kimura Y [15]
  • Madigan MT [15]
  • Wang-otomo ZY [15]
  • Yu LJ [14]
  • Wang-otomo Z-Y [10]
  • Nagashima KVP [9]
  • Yu L-J [9]
  • Purba ER [8]
  • Takaichi S [6]
  • Ji XC [5]
  • Takenaka S [5]
  • Inoue K [4]
  • Nagashima S [4]
  • Doi T [3]
  • Hamaguchi T [3]
  • Hiwatashi N [3]
  • Ji X-C [3]
  • Kawakami M [3]
  • Kawamura S [3]
  • Kikuchi R [3]
  • Kobayashi Y [3]
  • Maki-yonekura S [3]
  • Minamino A [3]
  • Mochizuki T [3]
  • Nakata K [3]
  • Negami T [3]
  • Terada T [3]
  • Yonekura K [3]
  • Harada A [2]
  • Inada K [2]
  • Inami M [2]
  • Iwasaki K [2]
  • Kobayashi A [2]
  • Matsushita R [2]
  • Nakamura N [2]
  • Ooya T [2]
  • Satoh I [2]
  • Takahashi A [2]
  • Dewa T [1]
  • Honda M [1]
  • Hosogi N [1]
  • Isawa Y [1]
  • Ishikawa I [1]
  • Izumida A [1]
  • Kishikawa J [1]
  • Kishikawa JI [1]
  • Kobayashi K [1]
  • Kojima R [1]
  • Kondo M [1]
  • Kurosawa K [1]
  • Matsuda Y [1]
  • Mino H [1]
  • Mio K [1]
  • Mitsuoka K [1]
  • Mori K [1]
  • Morishita R [1]
  • Nagasawa Y [1]
  • Nagashima VP [1]
  • Ohkubo T [1]
  • Okura Y [1]
  • Sasaki YC [1]
  • Seto R [1]
  • Tsukatani Y [1]

Author by ORCID

  • Tani K [18]
  • Wang-otomo ZY [14]
  • Kimura Y [14]
  • Yu LJ [10]
  • Takaichi S [6]
  • Kanno R [5]
  • Yonekura K [3]
  • Doi T [3]
  • Terada T [3]
  • Humbel BM [3]
  • Maki-yonekura S [3]
  • Hamaguchi T [3]
  • Iwasaki K [2]
  • Hosogi N [1]
  • Nagasawa Y [1]
  • Dewa T [1]
  • Kondo M [1]
  • Kishikawa JI [1]
  • Mino H [1]
  • Nagashima S [1]
  • Kojima R [1]

Journal

  • COMMUN BIOL [8]
  • NAT COMMUN [5]
  • BIOCHEMISTRY [4]
  • J BIOL CHEM [1]

Software

  • RELION [12]
  • CTFFIND [3]

Microscope

  • FEI TITAN KRIOS [9]
  • JEOL CRYO ARM 300 [4]
  • TFS KRIOS [3]
  • FEI TALOS ARCTICA [1]
  • FEI TECNAI ARCTICA [1]

Electron Source

  • FIELD EMISSION GUN [18]

Film or detector model

  • FEI FALCON III 4K X 4K [14]
  • GATAN K3 6K X 4K [4]

External links

  • PDB [17]
  • UniProt [16]
  • AlphaFold DB [14]
  • ChEBI [14]
  • ChEMBL [14]
  • DrugBank [14]
  • Gene Ontology [14]
  • Pfam [14]
  • InterPro [13]
  • PDBe-Kb [13]
  • SCOP2 [1]