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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yamaguchi, M."

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Search Summary

This query matches 51 Structures.

Refinements

Structure Determination Methodology

experimental (51)

Scientific Name of Source Organism

	Homo sapiens (20)
	Thermus thermophilus HB27 (8)
	Rhodospirillum rubrum (5)
	Bifidobacterium bifidum JCM 1254 (4)
	Kluyveromyces marxianus (4)
	Bifidobacterium longum subsp. longum (3)
	Saccharomyces cerevisiae (3)
	Saccharomyces cerevisiae S288C (2)
	Arabidopsis thaliana (1)
	Bos taurus (1)

More...

Taxonomy

	Eukaryota (29)
	Bacteria (22)
	Duplodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (44)
	ELECTRON MICROSCOPY (4)
	SOLUTION NMR (3)

Polymer Entity Type

Protein (51)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (8)
	2.0 - 2.5 (14)
	2.5 - 3.0 (9)
	3.0 - 3.5 (8)
	4.0 - 4.5 (1)
	> 4.5 (5)

Release Date

	2000 - 2004 (5)
	2005 - 2009 (3)
	2010 - 2014 (24)
	2015 - 2019 (11)
	2020 - 2024 (3)
	2025 - 2029 (5)

Enzyme Classification Name

	Transferases (13)
	Oxidoreductases (15)
	Translocases (14)
	Hydrolases (12)
	Ligases (2)

Membrane Protein Annotation

	MemProtMD (4)
	PDBTM (4)
	OPM (2)
	mpstruc (2)

Symmetry Type

	Asymmetric (43)
	Cyclic (12)

SCOP Classification

	Alpha and beta proteins (a/b) (9)
	Alpha and beta proteins (a+b) (6)
	Artifacts (4)
	All alpha proteins (2)

AllSelected

1 to 25 of 51 Structures

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1D4O \| pdb_00001d4o	Download File View File

CRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 ANGSTROMS RESOLUTION

Prasad, G.S., Sridhar, V., Yamaguchi, M., Hatefi, Y., Stout, C.D.

(1999) Nat Struct Biol 6: 1126-1131

Released	2000-01-20
Method	X-RAY DIFFRACTION 1.21 Å
Organisms	Bos taurus
Macromolecule	NADP(H) TRANSHYDROGENASE (protein)
Unique Ligands	NAP

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1L7D \| pdb_00001l7d	Download File View File

Crystal Structure of R. rubrum Transhydrogenase Domain I without Bound NAD(H)

Prasad, G.S., Wahlberg, M., Sridhar, V., Yamaguchi, M., Hatefi, Y., Stout, C.D.

(2002) Biochemistry 41: 12745-12754

Released	2002-11-20
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Rhodospirillum rubrum
Macromolecule	nicotinamide nucleotide Transhydrogenase, subunit alpha 1 (protein)

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1L7E \| pdb_00001l7e	Download File View File

Crystal Structure of R. rubrum Transhydrogenase Domain I with Bound NADH

Prasad, G.S., Wahlberg, M., Sridhar, V., Yamaguchi, M., Hatefi, Y., Stout, C.D.

(2002) Biochemistry 41: 12745-12754

Released	2002-11-20
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Rhodospirillum rubrum
Macromolecule	nicotinamide nucleotide Transhydrogenase, subunit alpha 1 (protein)
Unique Ligands	NAI

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1PNO \| pdb_00001pno	Download File View File

Crystal structure of R. rubrum transhydrogenase domain III bound to NADP

Sundaresan, V., Yamaguchi, M., Chartron, J., Stout, C.D.

(2003) Biochemistry 42: 12143-12153

Released	2003-11-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Rhodospirillum rubrum
Macromolecule	NAD(P) transhydrogenase subunit beta (protein)
Unique Ligands	NAP

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1PNQ \| pdb_00001pnq	Download File View File

Crystal structure of R. rubrum transhydrogenase domain III bound to NADPH

Sundaresan, V., Yamaguchi, M., Chartron, J., Stout, C.D.

(2003) Biochemistry 42: 12143-12153

Released	2003-11-11
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Rhodospirillum rubrum
Macromolecule	NAD(P) transhydrogenase subunit beta (protein)
Unique Ligands	NDP

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1XLT \| pdb_00001xlt	Download File View File

Crystal structure of Transhydrogenase [(domain I)2:domain III] heterotrimer complex

Sundaresan, V., Chartron, J., Yamaguchi, M., Stout, C.D.

(2005) J Mol Biology 346: 617-629

Released	2005-04-05
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Rhodospirillum rubrum
Macromolecule	NAD(P) transhydrogenase subunit alpha part 1 (protein) NAD(P) transhydrogenase subunit beta (protein)
Unique Ligands	NA, NAD, NDP
Unique branched monosaccharides	FRU, GLC

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2KWC \| pdb_00002kwc	Download File View File

The NMR structure of the autophagy-related protein Atg8

Kumeta, H., Watanabe, M., Nakatogawa, H., Yamaguchi, M., Ogura, K., Adachi, W., Fujioka, Y., Noda, N.N., Ohsumi, Y., Inagaki, F.

(2010) J Biomol NMR 47: 237-241

Released	2010-05-12
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Autophagy-related protein 8 (protein)

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2LDR \| pdb_00002ldr	Download File View File

Solution structure of Helix-RING domain of Cbl-b in the Tyr363 phosphorylated form

Kumeta, H., Kobashigawa, Y., Inagaki, F.

(2011) Proc Natl Acad Sci U S A 108: 20579-20584

Released	2011-12-14
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase CBL-B (protein)
Unique Ligands	ZN

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2LPU \| pdb_00002lpu	Download File View File

Solution structures of KmAtg10

Yamaguchi, M., Noda, N.N., Yamamoto, H., Shima, T., Kumeta, H., Kobashigawa, Y., Akada, R., Ohsumi, Y., Inagaki, F.

(2012) Structure 20: 1244-1254

Released	2012-08-01
Method	SOLUTION NMR
Organisms	Kluyveromyces marxianus
Macromolecule	KmAtg10 (protein)

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2ZDT \| pdb_00002zdt	Download File View File

Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor

Sogabe, S., Asano, Y., Fukumoto, S., Habuka, N., Fujishima, A.

(2008) Bioorg Med Chem 16: 4699-4714

Released	2008-09-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Mitogen-activated protein kinase 10 (protein)
Unique Ligands	46C, GOL

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2ZDU \| pdb_00002zdu	Download File View File

Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor

Sogabe, S., Ohra, T., Itoh, F., Habuka, N., Fujishima, A.

(2008) Bioorg Med Chem 16: 4715-4732

Released	2008-09-23
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Mitogen-activated protein kinase 10 (protein)
Unique Ligands	446

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3AXY \| pdb_00003axy	Download File View File

Structure of Florigen Activation Complex Consisting of Rice Florigen Hd3a, 14-3-3 Protein GF14 and Rice FD Homolog OsFD1

Ohki, I., Furuita, K., Hayashi, K., Taoka, K., Tsuji, H., Nakagawa, A., Shimamoto, K., Kojima, C.

(2011) Nature 476: 332-335

Released	2011-08-03
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Oryza sativa Japonica Group
Macromolecule	14-3-3-like protein GF14-C (protein) Protein HEADING DATE 3A (protein) Rice FD homolog OsFD1 (protein)

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3VGO \| pdb_00003vgo	Download File View File

Crystal structure of the N-terminal fragment of Cbl-b

Kobashigawa, Y., Noda, N.N., Inagaki, F.

(2011) Proc Natl Acad Sci U S A 108: 20579-20584

Released	2011-12-14
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase CBL-B (protein)

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3VQI \| pdb_00003vqi	Download File View File

Crystal structure of Kluyveromyces marxianus Atg5

Yamaguchi, M., Noda, N.N., Yamamoto, H., Shima, T., Kumeta, H., Kobashigawa, Y., Akada, R., Ohsumi, Y., Inagaki, F.

(2012) Structure 20: 1244-1254

Released	2012-08-01
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Kluyveromyces marxianus
Macromolecule	Atg5 (protein)
Unique Ligands	EPE, SO4

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3VX6 \| pdb_00003vx6	Download File View File

Crystal structure of Kluyveromyces marxianus Atg7NTD

Yamaguchi, M., Matoba, K., Sawada, R., Fujioka, Y., Nakatogawa, H., Yamamoto, H., Kobashigawa, Y., Hoshida, H., Akada, R., Ohsumi, Y., Noda, N.N., Inagaki, F.

(2012) Nat Struct Mol Biol 19: 1250-1256

Released	2012-11-14
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Kluyveromyces marxianus
Macromolecule	E1 (protein)

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3VX7 \| pdb_00003vx7	Download File View File

Crystal structure of Kluyveromyces marxianus Atg7NTD-Atg10 complex

Yamaguchi, M., Matoba, K., Sawada, R., Fujioka, Y., Nakatogawa, H., Yamamoto, H., Kobashigawa, Y., Hoshida, H., Akada, R., Ohsumi, Y., Noda, N.N., Inagaki, F.

(2012) Nat Struct Mol Biol 19: 1250-1256

Released	2012-11-14
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Kluyveromyces marxianus
Macromolecule	E1 (protein) E2 (protein)

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3VX8 \| pdb_00003vx8	Download File View File

Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex

Matoba, K., Fujioka, Y., Noda, N.N.

(2012) Nat Struct Mol Biol 19: 1250-1256

Released	2012-11-14
Method	X-RAY DIFFRACTION 3.11 Å
Organisms	Arabidopsis thaliana
Macromolecule	Autophagy-related protein 3 (protein) Ubiquitin-like modifier-activating enzyme atg7 (protein)

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3WUZ \| pdb_00003wuz	Download File View File

Crystal structure of the Ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha

Kuroki, K., Wang, J., Ose, T., Yamaguchi, M., Tabata, S., Maita, N., Nakamura, S., Kajikawa, M., Kogure, A., Satoh, T., Arase, H., Maenaka, K.

(2014) Proc Natl Acad Sci U S A 111: 8877-8882

Released	2014-06-11
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Homo sapiens
Macromolecule	Paired immunoglobulin-like type 2 receptor alpha (protein)
Unique Ligands	CIT, IPA

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3WV0 \| pdb_00003wv0	Download File View File

O-glycan attached to herpes simplex virus type 1 glycoprotein gB is recognized by the Ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha

Kuroki, K., Wang, J., Ose, T., Yamaguchi, M., Tabata, S., Maita, N., Nakamura, S., Kajikawa, M., Kogure, A., Satoh, T., Arase, H., Maenaka, K.

(2014) Proc Natl Acad Sci U S A 111: 8877-8882

Released	2014-06-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens Human alphaherpesvirus 1 strain KOS
Macromolecule	Envelope glycoprotein B (protein) Paired immunoglobulin-like type 2 receptor alpha (protein)
Unique Ligands	SO4
Unique branched monosaccharides	A2G, SIA

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4H04 \| pdb_00004h04	Download File View File

Lacto-N-biosidase from Bifidobacterium bifidum

Ito, T., Katayama, T., Wada, J., Suzuki, R., Ashida, H., Wakagi, T., Yamamoto, K., Fushinobu, S.

(2013) J Biological Chem 288: 11795-11806

Released	2013-03-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bifidobacterium bifidum JCM 1254
Macromolecule	Lacto-N-biosidase (protein)
Unique Ligands	SO4
Unique branched monosaccharides	GAL, NAG

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4IZH \| pdb_00004izh	Download File View File

Crystal Structure of the Alpha1 dimer of Thermus thermophilus Transhydrogenase in P6

Stout, C.D., Yamaguchi, M., Leung, J.

To be published

Released	2014-01-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermus thermophilus HB27
Macromolecule	NAD/NADP transhydrogenase alpha subunit 1 (protein)
Unique Ligands	GOL

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4IZI \| pdb_00004izi	Download File View File

Crystal Structure of the Alpha1 dimer of Thermus thermophilus Transhydrogenase in P4(3)

Stout, C.D., Yamaguchi, M., Leung, J.

To be published

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus HB27
Macromolecule	NAD/NADP transhydrogenase alpha subunit 1 (protein)
Unique Ligands	GOL

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4J16 \| pdb_00004j16	Download File View File

Crystal structure of Thermus thermophilus transhydrogenase heterotrimeric complex of the Alpha1 subunit dimer with the NADP binding domain (domain III) of the Beta subunit

Yamaguchi, M., Leung, J., Schurig Briccio, L.A., Gennis, R.B., Stout, C.D.

To be published

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.41 Å
Organisms	Thermus thermophilus HB27
Macromolecule	NAD(P) transhydrogenase subunit beta (protein) NAD/NADP transhydrogenase alpha subunit 1 (protein)
Unique Ligands	CL, GOL, NAD, NAP, PGE

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4J1T \| pdb_00004j1t	Download File View File

Crystal structure of Thermus thermophilus transhydrogenase heterotrimeric complex of the Alpha1 subunit dimer with the NADP binding domain (domain III) of the Beta subunit in P2(1)

Yamaguchi, M., Leung, J., Schurig Briccio, L.A., Gennis, R.B., Stout, C.D.

To be published

Released	2014-02-05
Method	X-RAY DIFFRACTION 2.37 Å
Organisms	Thermus thermophilus HB27
Macromolecule	NAD(P) transhydrogenase subunit beta (protein) NAD/NADP transhydrogenase alpha subunit 1 (protein)
Unique Ligands	GOL, NAD, NAP

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4JAW \| pdb_00004jaw	Download File View File

Crystal Structure of Lacto-N-Biosidase from Bifidobacterium bifidum complexed with LNB-thiazoline

Ito, T., Katayama, T., Stubbs, K.A., Fushinobu, S.

(2013) J Biological Chem 288: 11795-11806

Released	2013-03-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bifidobacterium bifidum JCM 1254
Macromolecule	Lacto-N-biosidase (protein)
Unique Ligands	GAL, NGT, SO4

1 to 25 of 51 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

1D4O | pdb_00001d4o

1L7D | pdb_00001l7d

1L7E | pdb_00001l7e

1PNO | pdb_00001pno

1PNQ | pdb_00001pnq

1XLT | pdb_00001xlt

2KWC | pdb_00002kwc

2LDR | pdb_00002ldr

2LPU | pdb_00002lpu

2ZDT | pdb_00002zdt

2ZDU | pdb_00002zdu

3AXY | pdb_00003axy

3VGO | pdb_00003vgo

3VQI | pdb_00003vqi

3VX6 | pdb_00003vx6

3VX7 | pdb_00003vx7

3VX8 | pdb_00003vx8

3WUZ | pdb_00003wuz

3WV0 | pdb_00003wv0

4H04 | pdb_00004h04

4IZH | pdb_00004izh

4IZI | pdb_00004izi

4J16 | pdb_00004j16

4J1T | pdb_00004j1t

4JAW | pdb_00004jaw