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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Tanaka, K."

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Search Summary

This query matches 59 Structures.

Refinements

Structure Determination Methodology

experimental (59)

Scientific Name of Source Organism

	Homo sapiens (22)
	Mus musculus (12)
	Actinia fragacea (9)
	Saccharomyces cerevisiae S288C (7)
	Saccharomyces cerevisiae (3)
	Bos taurus (2)
	Clostridium botulinum Prevot_594 (2)
	Grimontia hollisae (2)
	Influenza A virus (A/RI/5+/1957(H2N2)) (2)
	Pyrococcus furiosus DSM 3638 (2)

More...

Taxonomy

	Eukaryota (53)
	Bacteria (4)
	Archaea (2)
	Riboviria (2)
	Eukaryota (eukaryotes) (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (51)
	SOLUTION NMR (5)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (59)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (1)
	1.5 - 2.0 (19)
	2.0 - 2.5 (19)
	2.5 - 3.0 (6)
	3.0 - 3.5 (2)
	3.5 - 4.0 (3)
	4.0 - 4.5 (2)
	> 4.5 (1)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (4)
	2005 - 2009 (17)
	2010 - 2014 (19)
	2015 - 2019 (14)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (12)
	Ligases (9)
	Transferases (4)
	Oxidoreductases (1)
	Lyases (1)

Membrane Protein Annotation

	mpstruc (8)
	OPM (2)
	MemProtMD (1)
	PDBTM (1)

Symmetry Type

	Asymmetric (49)
	Cyclic (16)

SCOP Classification

	Alpha and beta proteins (a+b) (14)
	Artifacts (9)
	All beta proteins (9)
	Alpha and beta proteins (a/b) (1)
	All alpha proteins (6)
	Small proteins (1)

AllSelected

1 to 25 of 59 Structures

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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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1IYF \| pdb_00001iyf	Download File View File

Solution structure of ubiquitin-like domain of human parkin

Sakata, E., Yamaguchi, Y., Kurimoto, E., Kikuchi, J., Yokoyama, S., Kawahara, H., Yokosawa, H., Hattori, N., Mizuno, Y., Tanaka, K., Kato, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) EMBO Rep 4: 301-306

Released	2003-03-25
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	parkin (protein)

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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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1WXS \| pdb_00001wxs	Download File View File

Solution Structure of Ufm1, a ubiquitin-fold modifier

Sasakawa, H., Sakata, E., Yamaguchi, Y., Komatsu, M., Tatsumi, K., Kominami, E., Tanaka, K., Kato, K.

(2006) Biochem Biophys Res Commun 343: 21-26

Released	2006-04-18
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Ubiquitin-fold Modifier 1 (protein)

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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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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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1XPA \| pdb_00001xpa	Download File View File

SOLUTION STRUCTURE OF THE DNA-AND RPA-BINDING DOMAIN OF THE HUMAN REPAIR FACTOR XPA, NMR, 1 STRUCTURE

Ikegami, T., Kuraoka, I., Saijo, M., Kodo, N., Kyogoku, Y., Morikawa, K., Tanaka, K., Shirakawa, M.

(1998) Nat Struct Biol 5: 701-706

Released	1999-07-22
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	XPA (protein)
Unique Ligands	ZN

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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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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

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2RJ2 \| pdb_00002rj2	Download File View File

Crystal Structure of the Sugar Recognizing SCF Ubiquitin Ligase at 1.7 Resolution

Vaijayanthimala, S., Velmurugan, D., Mizushima, T., Yamane, T., Yoshida, Y., Tanaka, K.

To be published

Released	2008-10-14
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mus musculus
Macromolecule	F-box only protein 2 (protein)
Unique Ligands	CL, NI

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2RRU \| pdb_00002rru	Download File View File

Solution structure of the UBA omain of p62 and its interaction with ubiquitin

Isogai, S., Morimoto, D., Arita, K., Unzai, S., Tenno, T., Hasegawa, J., Sou, Y., Komatsu, M., Tanaka, K., Shirakawa, M., Tochio, H.

To be published

Released	2011-06-29
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Sequestosome-1 (protein)

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2Z5B \| pdb_00002z5b	Download File View File

Crystal Structure of a Novel Chaperone Complex for Yeast 20S Proteasome Assembly

Yashiroda, H., Mizushima, T., Okamoto, K., Kameyama, T., Hayashi, H., Kishimoto, T., Kasahara, M., Kurimoto, E., Sakata, E., Suzuki, A., Hirano, Y., Murata, S., Kato, K., Yamane, T., Tanaka, K.

(2008) Nat Struct Mol Biol 15: 228-236

Released	2008-01-22
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Protein YPL144W (protein) Uncharacterized protein YLR021W (protein)

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2Z5C \| pdb_00002z5c	Download File View File

Crystal Structure of a Novel Chaperone Complex for Yeast 20S Proteasome Assembly

Yashiroda, H., Mizushima, T., Okamoto, K., Kameyama, T., Hayashi, H., Kishimoto, T., Kasahara, M., Kurimoto, E., Sakata, E., Suzuki, A., Hirano, Y., Murata, S., Kato, K., Yamane, T., Tanaka, K.

(2008) Nat Struct Mol Biol 15: 228-236

Released	2008-01-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Proteasome component PUP2 (protein) Protein YPL144W (protein) Uncharacterized protein YLR021W (protein)

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2Z5E \| pdb_00002z5e	Download File View File

Crystal Structure of Proteasome Assembling Chaperone 3

Okamoto, K., Kurimoto, E., Sakata, E., Suzuki, A., Yamane, T., Hirano, Y., Murata, S., Tanaka, K., Kato, K.

(2008) Nat Struct Mol Biol 15: 228-236

Released	2008-02-19
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Proteasome Assembling Chaperone 3 (protein)

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2Z6O \| pdb_00002z6o	Download File View File

Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1

Mizushima , T., Tatsumi, K., Ozaki, Y., Kawakami, T., Suzuki, A., Ogasahara, K., Komatsu, M., Kominami, E., Tanaka, K., Yamane, T.

(2007) Biochem Biophys Res Commun 362: 1079-1084

Released	2007-09-25
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Ufm1-conjugating enzyme 1 (protein)
Unique Ligands	MG

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2Z6P \| pdb_00002z6p	Download File View File

Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1

Mizushima , T., Tatsumi, K., Ozaki, Y., Kawakami, T., Suzuki, A., Ogasahara, K., Komatsu, M., Kominami, E., Tanaka, K., Yamane, T.

(2007) Biochem Biophys Res Commun 362: 1079-1084

Released	2007-09-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Ufm1-conjugating enzyme 1 (protein)

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2Z84 \| pdb_00002z84	Download File View File

Insights from crystal and solution structures of mouse UfSP1

Ha, B.H., Ahn, H.C., Kang, S.H., Tanaka, K., Chung, C.H., Kim, E.E.

(2008) J Biological Chem 283: 14893-14900

Released	2008-03-04
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mus musculus
Macromolecule	Ufm1-specific protease 1 (protein)

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2ZJD \| pdb_00002zjd	Download File View File

Crystal Structure of LC3-p62 complex

Ichimura, Y., Kumanomidou, T., Sou, Y., Mizushima, T., Ezaki, J., Ueno, T., Kominami, E., Yamane, T., Tanaka, K., Komatsu, M.

(2008) J Biological Chem 283: 22847-22857

Released	2008-06-03
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Microtubule-associated proteins 1A/1B light chain 3B precursor (protein) undecameric peptide from Sequestosome-1 (protein)

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3A7S \| pdb_00003a7s	Download File View File

Catalytic domain of UCH37

Nishio, K., Kim, S.W., Kawai, K., Mizushima, T., Yamane, T., Hamazaki, J., Murata, S., Tanaka, K.

(2009) Biochem Biophys Res Commun

Released	2009-11-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin carboxyl-terminal hydrolase isozyme L5 (protein)
Unique Ligands	CL