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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kato, T."

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Search Summary

This query matches 105 Structures.

Refinements

Structure Determination Methodology

experimental (105)

Scientific Name of Source Organism

	Thermus thermophilus HB8 (21)
	Homo sapiens (17)
	Mus musculus (13)
	Thermococcus profundus (9)
	Chlamydomonas reinhardtii (6)
	Eucalyptus grandis (6)
	Salmonella enterica subsp. enterica serovar Typhimurium (6)
	synthetic construct (6)
	Nitratidesulfovibrio vulgaris str. 'Miyazaki F (5)
	Clostridioides difficile (4)

More...

Taxonomy

	Bacteria (49)
	Eukaryota (47)
	Archaea (9)
	other sequences (6)
	Riboviria (4)
	Duplodnaviria (3)

Experimental Method

	ELECTRON MICROSCOPY (72)
	X-RAY DIFFRACTION (32)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (105)
	DNA (4)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (4)
	2.0 - 2.5 (6)
	2.5 - 3.0 (22)
	3.0 - 3.5 (40)
	3.5 - 4.0 (23)
	4.0 - 4.5 (1)
	> 4.5 (4)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (2)
	2005 - 2009 (6)
	2010 - 2014 (6)
	2015 - 2019 (8)
	2020 - 2024 (77)
	2025 - 2029 (5)

Enzyme Classification Name

	Oxidoreductases (15)
	Translocases (19)
	Hydrolases (14)
	Transferases (1)

Membrane Protein Annotation

	PDBTM (28)
	mpstruc (22)
	OPM (10)
	MemProtMD (11)

Symmetry Type

	Asymmetric (68)
	Cyclic (30)
	Helical (6)
	Dihedral (1)

SCOP Classification

	All beta proteins (4)
	Multi-domain proteins (alpha and beta) (5)
	All alpha proteins (3)
	Alpha and beta proteins (a+b) (3)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 25 of 105 Structures

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1RCH \| pdb_00001rch	Download File View File

SOLUTION NMR STRUCTURE OF RIBONUCLEASE HI FROM ESCHERICHIA COLI, 8 STRUCTURES

Yamazaki, T., Fujiwara, M., Kato, T., Yamasaki, K., Nagayama, K.

(2000) Biol Pharm Bull 23: 1147

Released	1997-02-12
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	RIBONUCLEASE HI (protein)

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1V7M \| pdb_00001v7m	Download File View File

Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab

Feese, M.D., Tamada, T., Kato, Y., Maeda, Y., Hirose, M., Matsukura, Y., Shigematsu, H., Kato, T., Miyazaki, H., Kuroki, R.

(2004) Proc Natl Acad Sci U S A 101: 1816-1821

Released	2004-03-02
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Monoclonal TN1 Fab Heavy Chain (protein) Monoclonal TN1 Fab Light Chain (protein) Thrombopoietin (protein)

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1V7N \| pdb_00001v7n	Download File View File

Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab

Feese, M.D., Tamada, T., Kato, Y., Maeda, Y., Hirose, M., Matsukura, Y., Shigematsu, H., Kato, T., Miyazaki, H., Kuroki, R.

(2004) Proc Natl Acad Sci U S A 101: 1816-1821

Released	2004-03-02
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Monoclonal TN1 Fab Heavy Chain (protein) Monoclonal TN1 Fab Light Chain (protein) Thrombopoietin (protein)

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1WUH \| pdb_00001wuh	Download File View File

Three-Dimensional Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

To be published

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.24 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, NFC, SF4

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1WUI \| pdb_00001wui	Download File View File

Ultra-High resolution Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

(2005) Structure 13: 1635-1642

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.04 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, MRD, NFC, SF4

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1WUJ \| pdb_00001wuj	Download File View File

Three-Dimensional Structure Of The Ni-B State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

(2005) Structure 13: 1635-1642

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, NFO, SF4

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1WUK \| pdb_00001wuk	Download File View File

High resolution Structure Of The Oxidized State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

(2005) Structure 13: 1635-1642

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MRD, NFO, SF4

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1WUL \| pdb_00001wul	Download File View File

High Resolution Structure Of The Reduced State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

(2005) Structure 13: 1635-1642

Released	2005-12-07
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, MRD, NFR, SF4

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3A69 \| pdb_00003a69	Download File View File

Atomic model of the bacterial flagellar hook based on docking an X-ray derived structure and terminal two alpha-helices into an 7.1 angstrom resolution cryoEM map

Fujii, T., Kato, T., Namba, K.

(2009) Structure 17: 1485-1493

Released	2009-12-15
Method	ELECTRON MICROSCOPY 7.1 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	Flagellar hook protein flgE (protein)

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3J0R \| pdb_00003j0r	Download File View File

Model of a type III secretion system needle based on a 7 Angstrom resolution cryoEM map

Fujii, T., Cheung, M., Blanco, A., Kato, T., Blocker, A.J., Namba, K.

(2012) Proc Natl Acad Sci U S A 109: 4461-4466

Released	2012-02-29
Method	ELECTRON MICROSCOPY 7.7 Å
Organisms	Shigella flexneri
Macromolecule	Protein mxiH (protein)

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3VXV \| pdb_00003vxv	Download File View File

Crystal structure of methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence

Otani, J., Arita, K., Kato, T., Kinoshita, M., Ariyoshi, M., Shirakawa, M.

(2013) J Biological Chem 288: 6351-6362

Released	2013-01-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	Methyl-CpG-binding domain protein 4 (protein) DNA (5'-D(GPTPCPAPCPTPAPCP(5CM)PGPGPAPCPA)-3') (nucleic acid) DNA (5'-D(GPTPCPTPGPGPTPAPGPTPGPAPCPT)-3') (nucleic acid)
Unique Ligands	ACT, EDO

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3VXX \| pdb_00003vxx	Download File View File

Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence

Otani, J., Arita, K., Kato, T., Kinoshita, M., Ariyoshi, M., Shirakawa, M.

(2013) J Biological Chem 288: 6351-6362

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.204 Å
Organisms	Mus musculus
Macromolecule	Methyl-CpG-binding domain protein 4 (protein) DNA (5'-D(GPTPCP(5CM)PGPGPTPAPGPTPGPAPCPT)-3') (nucleic acid) DNA (5'-D(GPTPCPAPCPTPAPCP(5CM)PGPGPAPCPA)-3') (nucleic acid)
Unique Ligands	ACT, EDO

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3VYB \| pdb_00003vyb	Download File View File

Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence

Otani, J., Arita, K., Kato, T., Kinoshita, M., Ariyoshi, M., Shirakawa, M.

(2013) J Biological Chem 288: 6351-6362

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus
Macromolecule	Methyl-CpG-binding domain protein 4 (protein) DNA (5'-D(GPTPCP(5HC)PGPGPTPAPGPTPGPAPCPT)-3') (nucleic acid) DNA (5'-D(GPTPCPAPCPTPAPCP(5CM)PGPGPAPCPA)-3') (nucleic acid)
Unique Ligands	ACT, EDO

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3VYQ \| pdb_00003vyq	Download File View File

Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1

Otani, J., Arita, K., Kato, T., Kinoshita, M., Ariyoshi, M., Shirakawa, M.

(2013) J Biological Chem 288: 6351-6362

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.525 Å
Organisms	Mus musculus
Macromolecule	Methyl-CpG-binding domain protein 4 (protein) DNA (5'-D(APCPAPTPCP(5CM)PGPGPTPGPA)-3') (nucleic acid) DNA (5'-D(TPCPAPCPTPGPGPAPTPGPT)-3') (nucleic acid)
Unique Ligands	EDO, ZN

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4D3E \| pdb_00004d3e	Download File View File

Tetramer of IpaD, modified from 2J0O, fitted into negative stain electron microscopy reconstruction of the wild type tip complex from the type III secretion system of Shigella flexneri

Cheung, M., Shen, D.-K., Makino, F., Kato, T., Roehrich, D., Martinez-Argudo, I., Walker, M.L., Murillo, I., Liu, X., Pain, M., Brown, J., Frazer, G., Mantell, J., Mina, P., Todd, T., Sessions, R.B., Namba, K., Blocker, A.J.

(2015) Mol Microbiol 95: 31

Released	2014-12-10
Method	ELECTRON MICROSCOPY 24 Å
Organisms	Shigella flexneri 5a str. M90T
Macromolecule	INVASIN IPAD (protein)

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6IU3 \| pdb_00006iu3	Download File View File

Crystal structure of iron transporter VIT1 with zinc ions

Kato, T., Nishizawa, T., Yamashita, K., Taniguchi, R., Kumazaki, K., Ishitani, R., Nureki, O.

(2019) Nat Plants 5: 308-315

Released	2019-02-06
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Eucalyptus grandis
Macromolecule	VIT1 (protein)
Unique Ligands	OLC, ZN

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6IU4 \| pdb_00006iu4	Download File View File

Crystal structure of iron transporter VIT1 with cobalt ion

Kato, T., Nishizawa, T., Yamashita, K., Taniguchi, R., Kumazaki, K., Ishitani, R., Nureki, O.

(2019) Nat Plants 5: 308-315

Released	2019-02-06
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Eucalyptus grandis
Macromolecule	VIT1 (protein)
Unique Ligands	CO, ZN

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6IU5 \| pdb_00006iu5	Download File View File

Crystal structure of cytoplasmic metal binding domain with zinc ions

Kato, T., Nishizawa, T., Yamashita, K., Kumazaki, K., Ishitani, R., Nureki, O.

(2019) Nat Plants 5: 308-315

Released	2019-02-06
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Eucalyptus grandis
Macromolecule	VIT1 (protein)
Unique Ligands	CL, ZN

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6IU6 \| pdb_00006iu6	Download File View File

Crystal structure of cytoplasmic metal binding domain with nickel ions

Kato, T., Nishizawa, T., Yamashita, K., Kumazaki, K., Ishitani, R., Nureki, O.

(2019) Nat Plants 5: 308-315

Released	2019-02-06
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Eucalyptus grandis
Macromolecule	VIT1 (protein)
Unique Ligands	NI, ZN

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6IU8 \| pdb_00006iu8	Download File View File

Crystal structure of cytoplasmic metal binding domain with cobalt ions

Kato, T., Nishizawa, T., Yamashita, K., Kumazaki, K., Ishitani, R., Nureki, O.

(2019) Nat Plants 5: 308-315

Released	2019-02-06
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Eucalyptus grandis
Macromolecule	VIT1 (protein)
Unique Ligands	CO, ZN

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6IU9 \| pdb_00006iu9	Download File View File

Crystal structure of cytoplasmic metal binding domain with iron ions

Kato, T., Nishizawa, T., Yamashita, K., Kumazaki, K., Ishitani, R., Nureki, O.

(2019) Nat Plants 5: 308-315

Released	2019-02-06
Method	X-RAY DIFFRACTION 3 Å
Organisms	Eucalyptus grandis
Macromolecule	VIT1 (protein)
Unique Ligands	FE2, ZN

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6JN9 \| pdb_00006jn9	Download File View File

Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus

Oide, M., Kato, T., Oroguchi, T., Nakasako, M.

(2020) FEBS J 287: 3472-3493

Released	2020-02-12
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Thermococcus profundus
Macromolecule	Glutamate dehydrogenase (protein)
Unique Ligands	TRS

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6JNA \| pdb_00006jna	Download File View File

Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus

Oide, M., Kato, T., Oroguchi, T., Nakasako, M.

(2020) FEBS J 287: 3472-3493

Released	2020-02-12
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Thermococcus profundus
Macromolecule	Glutamate dehydrogenase (protein)
Unique Ligands	TRS

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6JNC \| pdb_00006jnc	Download File View File

Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus

Oide, M., Kato, T., Oroguchi, T., Nakasako, M.

(2020) FEBS J 287: 3472-3493

Released	2020-02-12
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Thermococcus profundus
Macromolecule	Glutamate dehydrogenase (protein)
Unique Ligands	TRS

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6JND \| pdb_00006jnd	Download File View File

Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus

Oide, M., Kato, T., Oroguchi, T., Nakasako, M.

(2020) FEBS J 287: 3472-3493

Released	2020-02-12
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Thermococcus profundus
Macromolecule	Glutamate dehydrogenase (protein)
Unique Ligands	TRS

1 to 25 of 105 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

1RCH | pdb_00001rch

1V7M | pdb_00001v7m

1V7N | pdb_00001v7n

1WUH | pdb_00001wuh

1WUI | pdb_00001wui

1WUJ | pdb_00001wuj

1WUK | pdb_00001wuk

1WUL | pdb_00001wul

3A69 | pdb_00003a69

3J0R | pdb_00003j0r

3VXV | pdb_00003vxv

3VXX | pdb_00003vxx

3VYB | pdb_00003vyb

3VYQ | pdb_00003vyq

4D3E | pdb_00004d3e

6IU3 | pdb_00006iu3

6IU4 | pdb_00006iu4

6IU5 | pdb_00006iu5

6IU6 | pdb_00006iu6

6IU8 | pdb_00006iu8

6IU9 | pdb_00006iu9

6JN9 | pdb_00006jn9

6JNA | pdb_00006jna

6JNC | pdb_00006jnc

6JND | pdb_00006jnd