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232,829 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kurimoto, E."

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Search Summary

This query matches 31 Structures.

Refinements

Structure Determination Methodology

experimental (31)

Scientific Name of Source Organism

	Homo sapiens (15)
	Saccharomyces cerevisiae S288C (13)
	Saccharomyces cerevisiae (7)

Taxonomy

Eukaryota (31)

Experimental Method

	ELECTRON MICROSCOPY (22)
	X-RAY DIFFRACTION (6)
	SOLUTION NMR (3)

Polymer Entity Type

Protein (31)

Refinement Resolution (Å)

	1.5 - 2.0 (3)
	2.0 - 2.5 (2)
	2.5 - 3.0 (2)
	3.5 - 4.0 (2)
	4.0 - 4.5 (3)
	> 4.5 (16)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (7)
	2010 - 2014 (2)
	2015 - 2019 (16)
	2020 - 2024 (5)

Enzyme Classification Name

	Hydrolases (24)
	Transferases (2)
	Ligases (2)

Symmetry Type

	Asymmetric (28)
	Cyclic (4)

SCOP Classification

	Alpha and beta proteins (a+b) (5)
	Artifacts (2)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 25 of 31 Structures

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1IYF	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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1WXS	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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2DOS	Download File View File

Structural basis for the recognition of Lys48-linked polyubiquitin chain by the Josephin domain of ataxin-3, a putative deubiquitinating enzyme

Sumiyoshi, A.

(2014) FEBS Lett 588: 4422-4430

Released	2007-05-22
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Ataxin-3 (protein)

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2Z5B	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	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	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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2ZCB	Download File View File

Crystal Structure of ubiquitin P37A/P38A

Kitahara, R., Tanaka, T., Sakata, E., Yamaguchi, Y., Kato, K., Yokoyama, S.

To be published

Released	2007-11-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin (protein)
Unique Ligands	ZN

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3A33	Download File View File

UbcH5b~Ubiquitin Conjugate

Sakata, E., Satoh, T., Yamamoto, S., Yamaguchi, Y., Yagi-Utsumi, M., Kurimoto, E., Wakatsuki, S., Kato, K.

(2010) Structure 18: 138-147

Released	2009-11-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	GOL

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3ALB	Download File View File

Cyclic Lys48-linked tetraubiquitin

Satoh, T., Sakata, E., Yamamoto, S., Yamaguchi, Y., Sumiyoshi, A., Wakatsuki, S., Kato, K.

(2010) Biochem Biophys Res Commun

Released	2010-08-25
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	ubiquitin (protein)
Unique Ligands	SO4

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3J47	Download File View File

Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid

Estrin, E., Lopez-Blanco, J.R., Chacon, P., Martin, A.

(2013) Structure 21: 1624-1635

Released	2013-08-28
Method	ELECTRON MICROSCOPY 7.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 8

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5A5B	Download File View File

Structure of the 26S proteasome-Ubp6 complex

Aufderheide, A., Beck, F., Stengel, F., Hartwig, M., Schweitzer, A., Pfeifer, G., Goldberg, A.L., Sakata, E., Baumeister, W., Foerster, F.

(2015) Proc Natl Acad Sci U S A 112: 8626

Released	2015-07-22
Method	ELECTRON MICROSCOPY 9.5 Å
Organisms	Homo sapiens Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 35

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5L4G	Download File View File

The human 26S proteasome at 3.9 A

Schweitzer, A., Aufderheide, A., Rudack, T., Beck, F.

(2016) Proc Natl Acad Sci U S A 113: 7816-7821

Released	2016-09-07
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 20
Unique Ligands	ADP, ATP, MG

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5L4K	Download File View File

The human 26S proteasome lid

Schweitzer, A., Aufderheide, A., Rudack, T., Beck, F.

(2016) Proc Natl Acad Sci U S A 113: 7816-7821

Released	2016-09-07
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 12

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5LN3	Download File View File

The human 26S Proteasome at 6.8 Ang.

Schweitzer, A., Beck, F., Sakata, E., Unverdorben, P.

(2017) Mol Cell Proteomics 16: 840-854

Released	2017-03-22
Method	ELECTRON MICROSCOPY 6.8 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 32

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5MP9	Download File View File

26S proteasome in presence of ATP (s1)

Wehmer, M., Rudack, T., Beck, F., Aufderheide, A., Pfeifer, G., Plitzko, J.M., Foerster, F., Schulten, K., Baumeister, W., Sakata, E.

(2017) Proc Natl Acad Sci U S A 114: 1305-1310

Released	2017-03-08
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 20
Unique Ligands	ADP, ATP, MG

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5MPA	Download File View File

26S proteasome in presence of ATP (s2)

Wehmer, M., Rudack, T., Beck, F., Aufderheide, A., Pfeifer, G., Plitzko, J.M., Foerster, F., Schulten, K., Baumeister, W., Sakata, E.

(2017) Proc Natl Acad Sci U S A 114: 1305-1310

Released	2017-03-08
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 20
Unique Ligands	ADP, ATP, MG

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5MPB	Download File View File

26S proteasome in presence of AMP-PNP (s3)

Wehmer, M., Rudack, T., Beck, F., Aufderheide, A., Pfeifer, G., Plitzko, J.M., Foerster, F., Schulten, K., Baumeister, W., Sakata, E.

(2017) Proc Natl Acad Sci U S A 114: 1305-1310

Released	2017-03-08
Method	ELECTRON MICROSCOPY 7.8 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 33
Unique Ligands	ADP, ANP, MG

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5MPC	Download File View File

26S proteasome in presence of BeFx (s4)

Wehmer, M., Rudack, T., Beck, F., Aufderheide, A., Pfeifer, G., Plitzko, J.M., Foerster, F., Schulten, K., Baumeister, W., Sakata, E.

(2017) Proc Natl Acad Sci U S A 114: 1305-1310

Released	2017-03-08
Method	ELECTRON MICROSCOPY 7.7 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 34
Unique Ligands	ADP, ATP, MG

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5MPD	Download File View File

26S proteasome in presence of ATP (s1)

Wehmer, M., Rudack, T., Beck, F., Aufderheide, A., Pfeifer, G., Plitzko, J.M., Foerster, F., Schulten, K., Baumeister, W., Sakata, E.

(2017) Proc Natl Acad Sci U S A 114: 1305-1310

Released	2017-03-08
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 13

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5MPE	Download File View File

26S proteasome in presence of ATP (s2)

Wehmer, M., Rudack, T., Beck, F., Aufderheide, A., Pfeifer, G., Plitzko, J.M., Foerster, F., Schulten, K., Baumeister, W., Sakata, E.

(2017) Proc Natl Acad Sci U S A 114: 1305-1310

Released	2017-03-08
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 13

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6FVT	Download File View File

26S proteasome, s1 state

Eisele, M.R., Reed, R.G., Rudack, T., Schweitzer, A., Beck, F., Nagy, I., Pfeifer, G., Plitzko, J.M., Baumeister, W., Tomko, R.J., Sakata, E.

(2018) Cell Rep 24: 1301-1315.e5

Released	2018-08-22
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 33
Unique Ligands	ADP, ATP, MG

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6FVU	Download File View File

26S proteasome, s2 state

Eisele, M.R., Reed, R.G., Rudack, T., Schweitzer, A., Beck, F., Nagy, I., Pfeifer, G., Plitzko, J.M., Baumeister, W., Tomko, R.J., Sakata, E.

(2018) Cell Rep 24: 1301-1315.e5

Released	2018-08-22
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 33
Unique Ligands	ADP, ATP, MG

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6FVV	Download File View File

26S proteasome, s3 state

Eisele, M.R., Reed, R.G., Rudack, T., Schweitzer, A., Beck, F., Nagy, I., Pfeifer, G., Plitzko, J.M., Baumeister, W., Tomko, R.J., Sakata, E.

(2018) Cell Rep 24: 1301-1315.e5

Released	2018-08-22
Method	ELECTRON MICROSCOPY 5.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 33
Unique Ligands	ADP, ATP, MG

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6FVW	Download File View File

26S proteasome, s4 state

Eisele, M.R., Reed, R.G., Rudack, T., Schweitzer, A., Beck, F., Nagy, I., Pfeifer, G., Plitzko, J.M., Baumeister, W., Tomko, R.J., Sakata, E.

(2018) Cell Rep 24: 1301-1315.e5

Released	2018-08-29
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 33
Unique Ligands	ADP, ATP, MG

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6FVX	Download File View File

26S proteasome, s5 state

Eisele, M.R., Reed, R.G., Rudack, T., Schweitzer, A., Beck, F., Nagy, I., Pfeifer, G., Plitzko, J.M., Baumeister, W., Tomko, R.J., Sakata, E.

(2018) Cell Rep 24: 1301-1315.e5

Released	2018-08-22
Method	ELECTRON MICROSCOPY 4.9 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 33
Unique Ligands	ADP, ATP, MG