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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Mizoguchi, A."

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Search Summary

This query matches 21 Structures.

Refinements

Structure Determination Methodology

experimental (21)

Scientific Name of Source Organism

	Halorhodospira halophila (3)
	Homo sapiens (3)
	Allochromatium vinosum DSM 180 (2)
	Candida albicans (2)
	Cereibacter sphaeroides f. sp. denitrificans (2)
	Mus musculus (2)
	Allochromatium tepidum (1)
	Blastochloris tepida (1)
	Cereibacter sphaeroides (1)
	Rattus norvegicus (1)

More...

Taxonomy

	Bacteria (14)
	Eukaryota (7)

Experimental Method

	ELECTRON MICROSCOPY (18)
	X-RAY DIFFRACTION (2)
	ELECTRON CRYSTALLOGRAPHY (1)

Polymer Entity Type

Protein (21)

Refinement Resolution (Å)

	2.0 - 2.5 (7)
	2.5 - 3.0 (10)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)
	> 4.5 (1)

Release Date

	2005 - 2009 (1)
	2020 - 2024 (17)
	2025 - 2029 (3)

Enzyme Classification Name

	Lyases (3)
	Hydrolases (2)

Membrane Protein Annotation

	PDBTM (15)
	MemProtMD (8)
	OPM (4)

Symmetry Type

	Asymmetric (16)
	Dihedral (3)
	Cyclic (2)

SCOP Classification

	Membrane and cell surface proteins and peptides (1)
	Alpha and beta proteins (a/b) (2)
	All alpha proteins (1)
	All beta proteins (1)

AllSelected

1 to 21 of 21 Structures

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Explore in 3D

2D57 \| pdb_00002d57	Download File View File

Double layered 2D crystal structure of AQUAPORIN-4 (AQP4M23) at 3.2 a resolution by electron crystallography

Hiroaki, Y., Tani, K., Kamegawa, A., Gyobu, N., Nishikawa, K., Suzuki, H., Walz, T., Sasaki, S., Mitsuoka, K., Kimura, K., Mizoguchi, A., Fujiyoshi, Y.

(2005) J Mol Biology 355: 628-639

Released	2006-01-31
Method	ELECTRON CRYSTALLOGRAPHY 3.2 Å
Organisms	Rattus norvegicus
Macromolecule	Aquaporin-4 (protein)

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7C9R \| pdb_00007c9r	Download File View File

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBRIO STRAIN 970

Tani, K., Kanno, R., Makino, Y., Hall, M., Takenouchi, M., Imanishi, M., Yu, L.-J., Overmann, J., Madigan, M.T., Kimura, Y., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.-Y.

(2020) Nat Commun 11: 4955-4955

Released	2020-10-07
Method	ELECTRON MICROSCOPY 2.82 Å
Organisms	Thiorhodovibrio frisius
Macromolecule	Unique protein chains: 10
Unique Ligands	8K6, BCL, BPH, CA, CDL, DGA, FE, H4X, HEM, LMT, MG, MQ8, PGV, UQ8

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7EBC \| pdb_00007ebc	Download File View File

Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae

Hiragi, K., Nishio, K., Moriyama, S., Hamaguchi, T., Mizoguchi, A., Yonekura, K., Tani, K., Mizushima, T.

(2021) J Struct Biol 213: 107748-107748

Released	2021-06-23
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Isocitrate lyase (protein)
Unique Ligands	MG, PG4

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7EBE \| pdb_00007ebe	Download File View File

Crystal structure of Isocitrate lyase-1 from Candida albicans

Hiragi, K., Nishio, K., Moriyama, S., Hamaguchi, T., Mizoguchi, A., Yonekura, K., Tani, K., Mizushima, T.

(2021) J Struct Biol 213: 107748-107748

Released	2021-06-23
Method	X-RAY DIFFRACTION 2.69 Å
Organisms	Candida albicans
Macromolecule	Isocitrate lyase (protein)
Unique Ligands	FMT, MG

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7EBF \| pdb_00007ebf	Download File View File

Cryo-EM structure of Isocitrate lyase-1 from Candida albicans

Hiragi, K., Nishio, K., Moriyama, S., Hamaguchi, T., Mizoguchi, A., Yonekura, K., Tani, K., Mizushima, T.

(2021) J Struct Biol 213: 107748-107748

Released	2021-06-23
Method	ELECTRON MICROSCOPY 2.63 Å
Organisms	Candida albicans
Macromolecule	Isocitrate lyase (protein)

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7EQD \| pdb_00007eqd	Download File View File

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLUM RUBRUM

Tani, K., Kanno, R., Ji, X.-C., Yu, L.-J., Hall, M., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.-Y.

(2021) Biochemistry

Released	2021-08-18
Method	ELECTRON MICROSCOPY 2.76 Å
Organisms	Rhodospirillum rubrum Rhodospirillum rubrum ATCC 11170
Macromolecule	Light-harvesting protein B-870 alpha chain (protein) Light-harvesting protein B-870 beta chain (protein) Photoreaction center protein H (protein) Reaction center protein L chain (protein) Reaction center protein M chain (protein)
Unique Ligands	07D, 08I, CDL, CRT, FE, LMT, PEF, PGV, RQ0, U10

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7F0L \| pdb_00007f0l	Download File View File

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES MONOMER

Tani, K., Nagashima, V.P., Kanno, R., Kawamura, S., Kikuchi, R., Ji, X.-C., Hall, M., Yu, L.-J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.-Y.

(2021) Nat Commun 12: 6300-6300

Released	2021-11-10
Method	ELECTRON MICROSCOPY 2.94 Å
Organisms	Cereibacter sphaeroides
Macromolecule	Unique protein chains: 8
Unique Ligands	BCL, BPH, CDL, FE, LDA, LMT, PGV, SPO, U10

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7VRJ \| pdb_00007vrj	Download File View File

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatium tepidum

Tani, K., Kobayashi, K., Hosogi, N., Ji, X.-C., Nagashima, S., Nagashima, K.V.P., Tsukatani, Y., Kanno, R., Hall, M., Yu, L.-J., Ishikawa, I., Okura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Kimura, Y., Wang-Otomo, Z.-Y.

(2022) J Biological Chem 298: 101967-101967

Released	2022-05-04
Method	ELECTRON MICROSCOPY 2.81 Å
Organisms	Allochromatium tepidum
Macromolecule	Unique protein chains: 9
Unique Ligands	BCL, BPH, CA, CDL, CRT, DGA, FE, HEC, LDA, LMT, MG, MQ8, PGV, PLM, UQ8

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7VY2 \| pdb_00007vy2	Download File View File

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES DIMER

Tani, K., Kanno, R., Kawamura, S., Kikuchi, R., Nagashima, K.V.P., Hall, M., Takahashi, A., Yu, L.-J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.-Y.

(2022) Nat Commun 13: 1904-1904

Released	2022-04-27
Method	ELECTRON MICROSCOPY 2.75 Å
Organisms	Cereibacter sphaeroides f. sp. denitrificans
Macromolecule	Unique protein chains: 7
Unique Ligands	BCL, BPH, CDL, FE, LDA, LMT, PGV, PTY, SPO, U10

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7VY3 \| pdb_00007vy3	Download File View File

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES LACKING PROTEIN-U

Tani, K., Kanno, R., Kawamura, S., Kikuchi, R., Nagashima, K.V.P., Hall, M., Takahashi, A., Yu, L.-J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.-Y.

(2022) Nat Commun 13: 1904-1904

Released	2022-04-27
Method	ELECTRON MICROSCOPY 2.63 Å
Organisms	Cereibacter sphaeroides f. sp. denitrificans
Macromolecule	Unique protein chains: 6
Unique Ligands	BCL, BPH, CDL, FE, LDA, LMT, PGV, PTY, SPO, U10

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7XXF \| pdb_00007xxf	Download File View File

Structure of photosynthetic LH1-RC super-complex of Rhodopila globiformis

Tani, K., Kanno, R., Kurosawa, K., Takaichi, S., Nagashima, K.V.P., Hall, M., Yu, L.-J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.-Y.

(2022) Commun Biol 5: 1197-1197

Released	2022-11-16
Method	ELECTRON MICROSCOPY 2.24 Å
Organisms	Rhodopila globiformis
Macromolecule	Unique protein chains: 7
Unique Ligands	BCL, BPH, CDL, FE, HEC, I7D, LMT, MQ9, PEE, PGV, U10

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7YML \| pdb_00007yml	Download File View File

Structure of photosynthetic LH1-RC super-complex of Rhodobacter capsulatus

Tani, K., Kanno, R., Ji, X.-C., Satoh, I., Kobayashi, Y., Nagashima, K.V.P., Hall, M., Yu, L.-J., Kimura, Y., Mizoguchi, A., Humbel, B.M., Madigan, M.T., Wang-Otomo, Z.-Y.

(2023) Nat Commun 14: 846-846

Released	2023-02-22
Method	ELECTRON MICROSCOPY 2.6 Å
Organisms	Rhodobacter capsulatus
Macromolecule	Unique protein chains: 6
Unique Ligands	BCL, BPH, FE, LDA, LMT, MYR, PEE, PGV, SPO, U10

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8WDU \| pdb_00008wdu	Download File View File

Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density

Tani, K., Kanno, R., Harada, A., Kobayashi, A., Minamino, A., Nakamura, N., Ji, X.-C., Purba, E.R., Hall, M., Yu, L.-J., Madigan, M.T., Mizoguchi, A., Iwasaki, K., Humbel, B.M., Kimura, Y., Wang-Otomo, Z.-Y.

(2024) Commun Biol 7: 176-176

Released	2024-02-21
Method	ELECTRON MICROSCOPY 2.24 Å
Organisms	Allochromatium vinosum DSM 180
Macromolecule	Unique protein chains: 9
Unique Ligands	BCL, BPH, CA, CDL, CRT, FE, HEM, LDA, LMT, MG, MQ8, PGV, PLM, UQ8, Z41

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8WDV \| pdb_00008wdv	Download File View File

Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by Ca2+-DEAE

(2024) Commun Biol 7: 176-176

Released	2024-02-21
Method	ELECTRON MICROSCOPY 2.24 Å
Organisms	Allochromatium vinosum DSM 180
Macromolecule	Unique protein chains: 9
Unique Ligands	BCL, BPH, CA, CDL, CRT, FE, HEM, LDA, LMT, MG, MQ8, PGV, PLM, UQ8, Z41

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8XWP \| pdb_00008xwp	Download File View File

Cryo-EM structure of ET-1 bound ETBR-DNGI complex

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

(2024) Commun Biol 7: 1303-1303

Released	2024-10-02
Method	ELECTRON MICROSCOPY 3.21 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 6

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8XWQ \| pdb_00008xwq	Download File View File

Cryo-EM structure of ET-1 bound ETBR-DNGI complex

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

(2024) Commun Biol 7: 1303-1303

Released	2024-10-02
Method	ELECTRON MICROSCOPY 4.6 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 6

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8Z81 \| pdb_00008z81	Download File View File

Photosynthetic LH2-LH1 complex from the purple bacterium Halorhodospira halophila

Tani, K., Nagashima, K.V.P., Kanno, R., Hiwatashi, N., Kawakami, M., Nakata, K., Nagashima, S., Inoue, K., Takaichi, S., Purba, E.R., Hall, M., Yu, L.-J., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Kimura, Y., Wang-Otomo, Z.-Y.

(2025) Nat Commun 16: 1410-1410

Released	2025-02-19
Method	ELECTRON MICROSCOPY 2.2 Å
Organisms	Halorhodospira halophila
Macromolecule	Unique protein chains: 6
Unique Ligands	BCL, CRT, LMT, PGV

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8Z82 \| pdb_00008z82	Download File View File

Photosynthetic LH1-RC-HiPIP complex from the purple bacterium Halorhodospira halophila

Tani, K., Kanno, R., Nagashima, K.V.P., Hiwatashi, N., Kawakami, M., Nakata, K., Nagashima, S., Inoue, K., Takaichi, S., Purba, E.R., Hall, M., Yu, L.-J., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Kimura, Y., Wang-Otomo, Z.-Y.

(2025) Commun Biol 8: 42-42

Released	2025-01-29
Method	ELECTRON MICROSCOPY 2.4 Å
Organisms	Halorhodospira halophila
Macromolecule	Unique protein chains: 9
Unique Ligands	BCL, BPH, CDL, CRT, FE, HEC, LMT, MG, MQ8, PGV, PLM, SF4, UQ8, Z41

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8Z83 \| pdb_00008z83	Download File View File

Photosynthetic LH1-RC complex from the purple bacterium Halorhodospira halophila

(2025) Commun Biol 8: 42-42

Released	2025-01-29
Method	ELECTRON MICROSCOPY 2.6 Å
Organisms	Halorhodospira halophila
Macromolecule	Unique protein chains: 8
Unique Ligands	BCL, BPH, CDL, CRT, FE, HEC, LMT, MG, MQ8, PGV, PLM, UQ8, Z41

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8ZRT \| pdb_00008zrt	Download File View File

Cryo-EM structure focused on the receptor of the ET-1 bound ETBR-DNGI complex

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

(2024) Commun Biol 7: 1303-1303

Released	2024-10-02
Method	ELECTRON MICROSCOPY 3.62 Å
Organisms	Homo sapiens
Macromolecule	Endothelin receptor type B (protein) Endothelin-1 (protein)

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9J2F \| pdb_00009j2f	Download File View File

Structure of photosynthetic LH1-RC complex from the purple bacterium Blastochloris tepida

Kimura, Y., Kanno, R., Mori, K., Matsuda, Y., Seto, R., Takenaka, S., Mino, H., Ohkubo, T., Honda, M., Sasaki, Y.C., Kishikawa, J., Mitsuoka, K., Mio, K., Hall, M., Purba, E.R., Mochizuki, T., Mizoguchi, A., Humbel, B.M., Madigan, M.T., Wang-Otomo, Z.-Y., Tani, K.

To be published

Released	2024-12-18
Method	ELECTRON MICROSCOPY 2.2 Å
Organisms	Blastochloris tepida
Macromolecule	Unique protein chains: 8
Unique Ligands	BCB, BPB, CDL, DGA, FE, HEC, LMT, MG, MQ7, NS0, NS5, PGV, UQ8

1 to 21 of 21 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

2D57 | pdb_00002d57

7C9R | pdb_00007c9r

7EBC | pdb_00007ebc

7EBE | pdb_00007ebe

7EBF | pdb_00007ebf

7EQD | pdb_00007eqd

7F0L | pdb_00007f0l

7VRJ | pdb_00007vrj

7VY2 | pdb_00007vy2

7VY3 | pdb_00007vy3

7XXF | pdb_00007xxf

7YML | pdb_00007yml

8WDU | pdb_00008wdu

8WDV | pdb_00008wdv

8XWP | pdb_00008xwp

8XWQ | pdb_00008xwq

8Z81 | pdb_00008z81

8Z82 | pdb_00008z82

8Z83 | pdb_00008z83

8ZRT | pdb_00008zrt

9J2F | pdb_00009j2f