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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Mizushima, T."

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Search Summary

This query matches 96 Structures.

Refinements

Structure Determination Methodology

experimental (96)

Scientific Name of Source Organism

	Homo sapiens (23)
	Mus musculus (12)
	Saccharomyces cerevisiae (12)
	Bos taurus (9)
	Saccharomyces cerevisiae S288C (8)
	Pyrococcus furiosus (7)
	Shigella flexneri (7)
	Pseudomonas putida (6)
	Achromobacter obae (3)
	Pyrococcus furiosus DSM 3638 (3)

More...

Taxonomy

	Eukaryota (66)
	Bacteria (20)
	Archaea (13)
	Eukaryota (eukaryotes) (1)

Experimental Method

	X-RAY DIFFRACTION (95)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (96)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (21)
	2.0 - 2.5 (41)
	2.5 - 3.0 (23)
	3.0 - 3.5 (5)
	3.5 - 4.0 (2)
	4.0 - 4.5 (1)

Release Date

	1995 - 1999 (4)
	2000 - 2004 (6)
	2005 - 2009 (29)
	2010 - 2014 (22)
	2015 - 2019 (23)
	2020 - 2024 (12)

Enzyme Classification Name

	Oxidoreductases (16)
	Hydrolases (13)
	Transferases (17)
	Translocases (6)
	Ligases (12)
	Lyases (7)
	Isomerases (5)

Membrane Protein Annotation

	MemProtMD (6)
	PDBTM (6)
	OPM (1)

Symmetry Type

	Asymmetric (61)
	Cyclic (31)
	Dihedral (10)

SCOP Classification

	Membrane and cell surface proteins and peptides (6)
	Alpha and beta proteins (a+b) (18)
	Alpha and beta proteins (a/b) (20)
	All beta proteins (20)
	All alpha proteins (15)
	Artifacts (10)
	Multi-domain proteins (alpha and beta) (2)
	Small proteins (6)

AllSelected

1 to 25 of 96 Structures

Page 1 of 4

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1DDZ \| pdb_00001ddz	Download File View File

X-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, PORPHYRIDIUM PURPUREUM R-1

Mitsuhashi, S., Mizushima, T., Yamashita, E., Miyachi, S., Tsukihara, T.

(2000) J Biological Chem 275: 5521-5526

Released	2000-03-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Porphyridium purpureum
Macromolecule	CARBONIC ANHYDRASE (protein)
Unique Ligands	ZN

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1IOF \| pdb_00001iof	Download File View File

X-RAY CRYSTALLINE STRUCTURES OF PYRROLIDONE CARBOXYL PEPTIDASE FROM A HYPERTHERMOPHILE, PYROCOCCUS FURIOSUS, AND ITS CYS-FREE MUTANT

Tanaka, H., Chinami, M., Ota, M., Tsukihara, T., Yutani, K.

(2001) J Biochem 130: 107-118

Released	2001-03-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pyrococcus furiosus
Macromolecule	PYRROLIDONE CARBOXYL PEPTIDASE (protein)

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1IOI \| pdb_00001ioi	Download File View File

x-ray crystalline structures of pyrrolidone carboxyl peptidase from a hyperthermophile, pyrococcus furiosus, and its cys-free mutant

Tanaka, H., Chinami, M., Ota, M., Tsukihara, T., Yutani, K.

(2001) J Biochem 130: 107-118

Released	2001-03-21
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Pyrococcus furiosus
Macromolecule	PYRROLIDONE CARBOXYL PEPTIDASE (protein)

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1IRU \| pdb_00001iru	Download File View File

Crystal Structure of the mammalian 20S proteasome at 2.75 A resolution

Unno, M., Mizushima, T., Morimoto, Y., Tomisugi, Y., Tanaka, K., Yasuoka, N., Tsukihara, T.

(2002) Structure 10: 609-618

Released	2002-05-22
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 14
Unique Ligands	MG

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1OCO \| pdb_00001oco	Download File View File

BOVINE HEART CYTOCHROME C OXIDASE IN CARBON MONOXIDE-BOUND STATE

Tsukihara, T., Yao, M.

(1998) Science 280: 1723-1729

Released	1999-07-22
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CMO, CU, HEA, MG, NA, ZN

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1OCR \| pdb_00001ocr	Download File View File

BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY REDUCED STATE

Tsukihara, T., Yao, M.

(1998) Science 280: 1723-1729

Released	1999-07-29
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CU, HEA, MG, NA, ZN

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1OCZ \| pdb_00001ocz	Download File View File

BOVINE HEART CYTOCHROME C OXIDASE IN AZIDE-BOUND STATE

Tsukihara, T., Yao, M.

(1998) Science 280: 1723-1729

Released	1999-07-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	AZI, CU, HEA, MG, NA, ZN

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1UMH \| pdb_00001umh	Download File View File

Structural basis of sugar-recognizing ubiquitin ligase

Mizushima, T., Hirao, T., Yoshida, Y., Lee, S.J., Chiba, T., Iwai, K., Yamaguchi, Y., Kato, K., Tsukihara, T., Tanaka, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Nat Struct Mol Biol 11: 365-370

Released	2004-04-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	F-box only protein 2 (protein)
Unique Ligands	NI

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1UMI \| pdb_00001umi	Download File View File

Structural basis of sugar-recognizing ubiquitin ligase

Mizushima, T., Hirao, T., Yoshida, Y., Lee, S.J., Chiba, T., Iwai, K., Yamaguchi, Y., Kato, K., Tsukihara, T., Tanaka, K.

(2004) Nat Struct Mol Biol 11: 365-370

Released	2004-04-06
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus
Macromolecule	F-box only protein 2 (protein)
Unique branched monosaccharides	NAG, NDG

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1WZV \| pdb_00001wzv	Download File View File

Crystal Structure of UbcH8

Mizushima, T., Suzuki, M., Teshima, N., Yamane, T., Murata, S., Tanaka, K.

To be published

Released	2005-03-22
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 L6 (protein)

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1WZW \| pdb_00001wzw	Download File View File

Crystal Structure of UbcH8

Mizushima, T., Suzuki, M., Teshima, N., Yamane, T., Murata, S., Tanaka, K.

To be published

Released	2005-03-22
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 L6 (protein)

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1X10 \| pdb_00001x10	Download File View File

Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192A) from a Hyperthermophile, Pyrococcus furiosus

Kaushik, J.K., Yamagata, Y., Ogasahara, K., Yutani, K.

(2006) Biochemistry 45: 7100-7112

Released	2006-06-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus furiosus
Macromolecule	Pyrrolidone-carboxylate peptidase (protein)

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1X12 \| pdb_00001x12	Download File View File

Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192D) from a Hyperthermophile, Pyrococcus furiosus

Kaushik, J.K., Yamagata, Y., Ogasahara, K., Yutani, K.

(2006) Biochemistry 45: 7100-7112

Released	2006-06-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus furiosus
Macromolecule	Pyrrolidone-carboxylate peptidase (protein)

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1X23 \| pdb_00001x23	Download File View File

Crystal structure of ubch5c

Nakanishi, M., Teshima, N., Mizushima, T., Murata, S., Tanaka, K., Yamane, T.

To be published

Released	2005-05-03
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 D3 (protein)

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1Z8T \| pdb_00001z8t	Download File View File

Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192Q) from a Hyperthermophile, Pyrococcus furiosus

Kaushik, J.K., Yamagata, Y., Ogasahara, K., Yutani, K.

(2006) Biochemistry 45: 7100-7112

Released	2006-06-13
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pyrococcus furiosus
Macromolecule	Pyrrolidone-carboxylate peptidase (protein)

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1Z8W \| pdb_00001z8w	Download File View File

Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192I) from a Hyperthermophile, Pyrococcus furiosus

Kaushik, J.K., Yamagata, Y., Ogasahara, K., Yutani, K.

(2006) Biochemistry 45: 7100-7112

Released	2006-06-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus furiosus
Macromolecule	Pyrrolidone-carboxylate peptidase (protein)

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1Z8X \| pdb_00001z8x	Download File View File

Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192V) from a Hyperthermophile, Pyrococcus furiosus

Kaushik, J.K., Yamagata, Y., Ogasahara, K., Yutani, K.

(2006) Biochemistry 45: 7100-7112

Released	2006-06-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus furiosus
Macromolecule	Pyrrolidone-carboxylate peptidase (protein)

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2B9U \| pdb_00002b9u	Download File View File

Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from sulfolobus tokodaii

Rajakannan, V., Kondo, K., Mizushima, T., Suzuki, A., Yamane, T.

To be published

Released	2006-10-13
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase (protein)

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2D1I \| pdb_00002d1i	Download File View File

Structure of human Atg4b

Kumanomidou, T., Mizushima, T., Komatsu, M., Suzuki, A., Tanida, I., Sou, Y.S., Ueno, T., Kominami, E., Tanaka, K., Yamane, T.

(2006) J Mol Biology 355: 612-618

Released	2006-01-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Cysteine protease APG4B (protein)

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2DYR \| pdb_00002dyr	Download File View File

Bovine heart cytochrome C oxidase at the fully oxidized state

Shinzawa-Itoh, K., Aoyama, H., Muramoto, K., Kurauchi, T., Mizushima, T., Yamashita, E., Tsukihara, T., Yoshikawa, S.

(2007) EMBO J 26: 1713-1725

Released	2007-04-03
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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2DYS \| pdb_00002dys	Download File View File

Bovine heart cytochrome C oxidase modified by DCCD

Shinzawa-Itoh, K., Aoyama, H., Muramoto, K., Kurauchi, T., Mizushima, T., Yamashita, E., Tsukihara, T., Yoshikawa, S.

(2007) EMBO J 26: 1713-1725

Released	2007-04-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DCW, DMU, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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2E31 \| pdb_00002e31	Download File View File

Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase

Mizushima, T., Yoshida, Y., Kumanomidou, T., Hasegawa, Y., Yamane, T., Tanaka, K.

(2007) Proc Natl Acad Sci U S A 104: 5777-5781

Released	2007-03-20
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	F-box only protein 2 (protein) S-phase kinase-associated protein 1A (protein)

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2E32 \| pdb_00002e32	Download File View File

Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase

Mizushima, T., Yoshida, Y., Kumanomidou, T., Hasegawa, Y., Yamane, T., Tanaka, K.

(2007) Proc Natl Acad Sci U S A 104: 5777-5781

Released	2007-03-20
Method	X-RAY DIFFRACTION 3.52 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	F-box only protein 2 (protein) S-phase kinase-associated protein 1A (protein)

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2E33 \| pdb_00002e33	Download File View File

Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase

Mizushima, T., Yoshida, Y., Kumanomidou, T., Hasegawa, Y., Yamane, T., Tanaka, K.

(2007) Proc Natl Acad Sci U S A 104: 5777-5781

Released	2007-03-20
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Bos taurus Mus musculus
Macromolecule	F-box only protein 2 (protein) Ribonuclease pancreatic (protein)
Unique branched monosaccharides	BMA, MAN, NAG