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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Watanabe, M."

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Search Summary

This query matches 68 Structures.

Refinements

Structure Determination Methodology

experimental (68)

Scientific Name of Source Organism

	Homo sapiens (7)
	metagenome (6)
	Geobacillus stearothermophilus (5)
	Talaromyces pinophilus CF-2612 (5)
	Escherichia coli K-12 (4)
	Pyrococcus horikoshii (4)
	Streptomyces venezuelae (4)
	Talaromyces pinophilus (4)
	Aspergillus oryzae RIB40 (3)
	Caenorhabditis elegans (3)

More...

Taxonomy

	Eukaryota (29)
	Bacteria (18)
	Archaea (9)
	unclassified sequences (9)

Experimental Method

	X-RAY DIFFRACTION (58)
	ELECTRON MICROSCOPY (7)
	SOLUTION NMR (3)

Polymer Entity Type

Protein (68)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (21)
	2.0 - 2.5 (17)
	2.5 - 3.0 (9)
	3.0 - 3.5 (5)
	3.5 - 4.0 (5)
	> 4.5 (1)

Release Date

	2000 - 2004 (6)
	2005 - 2009 (8)
	2010 - 2014 (9)
	2015 - 2019 (15)
	2020 - 2024 (28)
	2025 - 2029 (2)

Enzyme Classification Name

	Hydrolases (16)
	Transferases (8)
	Oxidoreductases (2)
	Isomerases (2)

Membrane Protein Annotation

	PDBTM (7)
	mpstruc (7)
	MemProtMD (6)
	OPM (6)

Symmetry Type

	Asymmetric (24)
	Cyclic (38)
	Dihedral (8)

SCOP Classification

	All beta proteins (8)
	Alpha and beta proteins (a/b) (5)
	Alpha and beta proteins (a+b) (9)
	All alpha proteins (3)
	Artifacts (1)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 68 Structures

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1IQ8 \| pdb_00001iq8	Download File View File

Crystal Structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii

Ishitani, R., Nureki, O., Fukai, S., Kijimoto, T., Nameki, N., Watanabe, M., Kondo, H., Sekine, M., Okada, N., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Mol Biology 318: 665-677

Released	2002-05-22
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pyrococcus horikoshii
Macromolecule	ARCHAEOSINE TRNA-GUANINE TRANSGLYCOSYLASE (protein)
Unique Ligands	MG, ZN

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1IT7 \| pdb_00001it7	Download File View File

Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine

Ishitani, R., Nureki, O., Fukai, S., Kijimoto, T., Nameki, N., Watanabe, M., Kondo, H., Sekine, M., Okada, N., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Mol Biology 318: 665-677

Released	2002-05-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Archaeosine tRNA-guanine transglycosylase (protein)
Unique Ligands	GUN, MG, ZN

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1IT8 \| pdb_00001it8	Download File View File

Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0

Ishitani, R., Nureki, O., Fukai, S., Kijimoto, T., Nameki, N., Watanabe, M., Kondo, H., Sekine, M., Okada, N., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2002) J Mol Biology 318: 665-677

Released	2002-05-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pyrococcus horikoshii
Macromolecule	archaeosine tRNA-guanine transglycosylase (protein)
Unique Ligands	MG, PQ0, ZN

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1UAW \| pdb_00001uaw	Download File View File

Solution structure of the N-terminal RNA-binding domain of mouse Musashi1

Miyanoiri, Y., Kobayashi, H., Watanabe, M., Ikeda, T., Nagata, T., Okano, H., Uesugi, S., Katahira, M.

(2003) J Biological Chem 278: 41309-41315

Released	2004-03-24
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	mouse-musashi-1 (protein)

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1V9Y \| pdb_00001v9y	Download File View File

Crystal Structure of the heme PAS sensor domain of Ec DOS (ferric form)

Kurokawa, H., Lee, D.S., Watanabe, M., Sagami, I., Mikami, B., Raman, C.S., Shimizu, T.

(2004) J Biological Chem 279: 20186-20193

Released	2004-05-25
Method	X-RAY DIFFRACTION 1.32 Å
Organisms	Escherichia coli K-12
Macromolecule	Heme pas sensor protein (protein)
Unique Ligands	HEM

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1V9Z \| pdb_00001v9z	Download File View File

Crystal Structure of the heme PAS sensor domain of Ec DOS (Ferrous Form)

Kurokawa, H., Lee, D.S., Watanabe, M., Sagami, I., Mikami, B., Raman, C.S., Shimizu, T.

(2004) J Biological Chem 279: 20186-20193

Released	2004-05-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli K-12
Macromolecule	Heme pas sensor protein (protein)
Unique Ligands	HEM

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1VB6 \| pdb_00001vb6	Download File View File

Crystal Structure of the heme PAS sensor domain of Ec DOS (oxygen-bound form)

Kurokawa, H., Watanabe, M., Sagami, I., Mikami, B., Shimizu, T.

To be published

Released	2005-04-19
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Escherichia coli K-12
Macromolecule	Heme pas sensor protein (protein)
Unique Ligands	HEM, OXY

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2CZW \| pdb_00002czw	Download File View File

Crystal structure analysis of protein component Ph1496p of P.horikoshii ribonuclease P

Fukuhara, H., Kifusa, M., Watanabe, M., Terada, A., Honda, T., Numata, T., Kakuta, Y., Kimura, M.

(2006) Biochem Biophys Res Commun 343: 956-964

Released	2006-04-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Pyrococcus horikoshii
Macromolecule	50S ribosomal protein L7Ae (protein)

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2DVY \| pdb_00002dvy	Download File View File

Crystal structure of restriction endonucleases PabI

Miyazono, K., Watanabe, M., Kamo, M., Sawasaki, T., Nagata, K., Endo, Y., Tanokura, M., Kobayashi, I.

(2007) Nucleic Acids Res 35: 1908-1918

Released	2007-05-08
Method	X-RAY DIFFRACTION 3 Å
Organisms	Pyrococcus abyssi
Macromolecule	Restriction endonuclease PabI (protein)

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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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2YU0 \| pdb_00002yu0	Download File View File

Solution structures of the PAAD_DAPIN domain of mus musculus interferon-activatable protein 205

Sato, M., Tochio, N., Koshiba, S., Watanabe, M., Harada, T., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-02-19
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Interferon-activable protein 205 (protein)

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2ZCZ \| pdb_00002zcz	Download File View File

Crystal structures and thermostability of mutant TRAP3 A7 (ENGINEERED TRAP)

Watanabe, M., Mishima, Y., Yamashita, I., Park, S.Y., Tame, J.R.H., Heddle, J.G.

(2008) Protein Sci 17: 518-526

Released	2008-04-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	Transcription attenuation protein mtrB (protein)
Unique Ligands	TRP

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2ZD0 \| pdb_00002zd0	Download File View File

Crystal structures and thermostability of mutant TRAP3 A5 (ENGINEERED TRAP)

Watanabe, M., Mishima, Y., Yamashita, I., Park, S.Y., Tame, J.R.H., Heddle, J.G.

(2008) Protein Sci 17: 518-526

Released	2008-04-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	Transcription attenuation protein mtrB (protein)
Unique Ligands	TRP

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2ZP8 \| pdb_00002zp8	Download File View File

The Nature of the TRAP:Anti-TRAP complex

Watanabe, M., Heddle, J.G., Unzai, S., Akashi, S., Park, S.Y., Tame, J.R.H.

(2009) Proc Natl Acad Sci U S A 106: 2176-2181

Released	2009-02-03
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Bacillus subtilis Geobacillus stearothermophilus
Macromolecule	Transcription attenuation protein mtrB (protein) Tryptophan RNA-binding attenuator protein-inhibitory protein (protein)
Unique Ligands	TRP, ZN

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2ZP9 \| pdb_00002zp9	Download File View File

The Nature of the TRAP:Anti-TRAP complex

Watanabe, M., Heddle, J.G., Unzai, S., Akashi, S., Park, S.Y., Tame, J.R.H.

(2009) Proc Natl Acad Sci U S A 106: 2176-2181

Released	2009-02-03
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Bacillus subtilis Geobacillus stearothermophilus
Macromolecule	Transcription attenuation protein mtrB (protein) Tryptophan RNA-binding attenuator protein-inhibitory protein (protein)
Unique Ligands	TRP, ZN

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3AJY \| pdb_00003ajy	Download File View File

Crystal Structure of Ancestral Congerin Con-anc

Konno, A., Kitagawa, A., Watanabe, M., Ogawa, T., Shirai, T.

(2011) Structure 19: 711-721

Released	2011-05-18
Method	X-RAY DIFFRACTION 2.01 Å
Macromolecule	Ancestral congerin Con-anc (protein)
Unique branched monosaccharides	BGC, GAL

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3AJZ \| pdb_00003ajz	Download File View File

Crystal Structure of Ancestral Congerin Con-anc

Konno, A., Kitagawa, A., Watanabe, M., Ogawa, T., Shirai, T.

(2011) Structure 19: 711-721

Released	2011-05-18
Method	X-RAY DIFFRACTION 1.5 Å
Macromolecule	Ancestral congerin Con-anc (protein)
Unique branched monosaccharides	BGC, GAL

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3AK0 \| pdb_00003ak0	Download File View File

Crystal Structure of Ancestral Congerin Con-anc'-N28K

Konno, A., Kitagawa, A., Watanabe, M., Ogawa, T., Shirai, T.

(2011) Structure 19: 711-721

Released	2011-05-18
Method	X-RAY DIFFRACTION 1.59 Å
Macromolecule	Ancestral congerin Con-anc (protein)
Unique branched monosaccharides	BGC, GAL

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3AQD \| pdb_00003aqd	Download File View File

Unliganded TRAP

Malay, A.A.D., Watanabe, M., Heddle, J.G., Tame, J.R.H.

To be published

Released	2010-12-29
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	Transcription attenuation protein mtrB (protein)

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3ST7 \| pdb_00003st7	Download File View File

Crystal Structure of capsular polysaccharide assembling protein CapF from staphylococcus aureus

Miyafusa, T., Tanaka, Y., Kuroda, M., Yao, M., Watanabe, M., Ohta, T., Tanaka, I., Caaveiro, J.M.M., Tsumoto, K.

(2012) Biochem J 443: 671-680

Released	2012-02-15
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Staphylococcus aureus subsp. aureus Mu50
Macromolecule	Capsular polysaccharide synthesis enzyme Cap5F (protein)
Unique Ligands	GOL, ZN

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3VU3 \| pdb_00003vu3	Download File View File

Crystal structure of the Hfq and catalase HPII complex

Watanabe, M., Yonekura, K.

(2013) PLoS One 8: e78216-e78216

Released	2013-11-20
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Escherichia coli K-12
Macromolecule	Catalase HPII (protein) Protein hfq (protein)
Unique Ligands	HEM