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232,829 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yagi-Utsumi, M."

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Search Summary

This query matches 14 Structures.

Refinements

Structure Determination Methodology

experimental (14)

Scientific Name of Source Organism

	Homo sapiens (10)
	Pyrococcus furiosus DSM 3638 (3)
	Saccharomyces cerevisiae S288C (3)
	Mycothermus thermophilus (1)

Taxonomy

	Eukaryota (13)
	Archaea (3)

Experimental Method

	X-RAY DIFFRACTION (12)
	SOLID-STATE NMR (1)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (14)

Refinement Resolution (Å)

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

Release Date

	2005 - 2009 (1)
	2010 - 2014 (4)
	2015 - 2019 (7)
	2020 - 2024 (2)

Enzyme Classification Name

	Transferases (1)
	Isomerases (1)
	Ligases (1)

Symmetry Type

	Asymmetric (10)
	Cyclic (4)
	Helical (1)

SCOP Classification

	All beta proteins (4)
	Artifacts (2)
	Alpha and beta proteins (a/b) (1)
	Alpha and beta proteins (a+b) (2)

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1 to 14 of 14 Structures

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2RSU	Download File View File

Alternative structure of Ubiquitin

Kitazawa, S., Kameda, T., Yagi-Utsumi, M., Kato, K., Kitahara, R.

(2013) Biochemistry 52: 1874-1885

Released	2013-03-27
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Ubiquitin (protein)

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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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3WHJ	Download File View File

Crystal structure of Nas2 N-terminal domain

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.

(2014) Structure 22: 731-743

Released	2014-03-26
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Probable 26S proteasome regulatory subunit p27 (protein)
Unique Ligands	CD, SO4

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3WHK	Download File View File

Crystal structure of PAN-Rpt5C chimera

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.

(2014) Structure 22: 731-743

Released	2014-03-26
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus furiosus DSM 3638 Saccharomyces cerevisiae S288C
Macromolecule	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A (protein)
Unique Ligands	ATP

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3WHL	Download File View File

Crystal structure of Nas2 N-terminal domain complexed with PAN-Rpt5C chimera

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.

(2014) Structure 22: 731-743

Released	2014-03-26
Method	X-RAY DIFFRACTION 4 Å
Organisms	Pyrococcus furiosus DSM 3638 Saccharomyces cerevisiae S288C
Macromolecule	Probable 26S proteasome regulatory subunit p27 (protein) Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A (protein)
Unique Ligands	ATP

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4YGB	Download File View File

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-free form

Satoh, T., Nishio, M., Yagi-Utsumi, M., Suzuki, K., Anzai, T., Mizushima, T., Kamiya, Y., Kato, K.

(2020) Acta Crystallogr F Struct Biol Commun 76: 216-221

Released	2016-04-06
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Multiple coagulation factor deficiency protein 2 (protein) Protein ERGIC-53 (protein)
Unique Ligands	CA, GOL

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4YGC	Download File View File

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 1

Satoh, T., Nishio, M., Yagi-Utsumi, M., Suzuki, K., Anzai, T., Mizushima, T., Kamiya, Y., Kato, K.

(2020) Acta Crystallogr F Struct Biol Commun 76: 216-221

Released	2016-04-06
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Multiple coagulation factor deficiency protein 2 (protein) Protein ERGIC-53 (protein)
Unique Ligands	CA, CL

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4YGD	Download File View File

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2

Satoh, T., Nishio, M., Yagi-Utsumi, M., Suzuki, K., Anzai, T., Mizushima, T., Kamiya, Y., Kato, K.

(2020) Acta Crystallogr F Struct Biol Commun 76: 216-221

Released	2016-04-06
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Homo sapiens
Macromolecule	Multiple coagulation factor deficiency protein 2 (protein) Protein ERGIC-53 (protein)
Unique Ligands	CA, CL

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4YGE	Download File View File

Crystal structure of ERGIC-53/MCFD2, trigonal calcium-bound form 2

Satoh, T., Nishio, M., Yagi-Utsumi, M., Suzuki, K., Anzai, T., Mizushima, T., Kamiya, Y., Kato, K.

(2020) Acta Crystallogr F Struct Biol Commun 76: 216-221

Released	2016-04-06
Method	X-RAY DIFFRACTION 3.05 Å
Organisms	Homo sapiens
Macromolecule	Multiple coagulation factor deficiency protein 2 (protein) Protein ERGIC-53 (protein)
Unique Ligands	CA, CL

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5CRW	Download File View File

Crystal structure of the b'-a' domain of oxidized protein disulfide isomerase complexed with alpha-synuclein peptide (31-41)

Yagi-Utsumi, M., Satoh, T., Kato, K.

(2015) Sci Rep 5: 13909-13909

Released	2015-09-09
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens Mycothermus thermophilus
Macromolecule	Peptide from Alpha-synuclein (protein) Protein disulfide-isomerase (protein)