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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Ogura, T."

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Search Summary

This query matches 13 Structures.

Refinements

Structure Determination Methodology

experimental (13)

Scientific Name of Source Organism

	Bos taurus (7)
	Hydrogenobacter thermophilus TK-6 (2)
	Pseudomonas aeruginosa PAO1 (2)
	Sus scrofa (2)
	Escherichia coli (1)
	Mus musculus (1)
	Thermochaetoides thermophila (1)

Taxonomy

	Eukaryota (10)
	Bacteria (3)

Experimental Method

	X-RAY DIFFRACTION (10)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (13)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (4)
	2.0 - 2.5 (4)
	2.5 - 3.0 (1)
	> 4.5 (3)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (1)
	2010 - 2014 (4)
	2015 - 2019 (6)
	2020 - 2024 (1)

Enzyme Classification Name

	Oxidoreductases (7)
	Translocases (7)
	Hydrolases (3)

Membrane Protein Annotation

	MemProtMD (7)
	PDBTM (7)
	OPM (1)

Symmetry Type

	Asymmetric (12)
	Cyclic (1)
	Helical (1)

SCOP Classification

	Membrane and cell surface proteins and peptides (7)
	All alpha proteins (9)
	All beta proteins (7)
	Small proteins (7)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 13 of 13 Structures

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1LV7 \| pdb_00001lv7	Download File View File

Crystal Structure of the AAA domain of FtsH

Krzywda, S., Brzozowski, A.M., Verma, C., Karata, K., Ogura, T., Wilkinson, A.J.

(2002) Structure 10: 1073-1083

Released	2002-10-09
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Escherichia coli
Macromolecule	FtsH (protein)
Unique Ligands	SO4

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2ZXW \| pdb_00002zxw	Download File View File

Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset)

Aoyama, H., Muramoto, K., Shinzawa-Itoh, K., Hirata, K., Yamashita, E., Tsukihara, T., Ogura, T., Yoshikawa, S.

(2009) Proc Natl Acad Sci U S A 106: 2165-2169

Released	2009-02-24
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PER, PGV, PSC, TGL, UNX, ZN

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3ABL \| pdb_00003abl	Download File View File

Bovine heart cytochrome c oxidase at the fully oxidized state (15-s X-ray exposure dataset)

Aoyama, H., Muramoto, K., Shinzawa-Itoh, K., Yamashita, E., Tsukihara, T., Ogura, T., Yoshikawa, S.

(2009) Proc Natl Acad Sci U S A 106: 2165-2169

Released	2010-01-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PER, PGV, PSC, TGL, UNX, ZN

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3ABM \| pdb_00003abm	Download File View File

Bovine heart cytochrome c oxidase at the fully oxidized state (200-s X-ray exposure dataset)

Aoyama, H., Muramoto, K., Shinzawa-Itoh, K., Yamashita, E., Tsukihara, T., Ogura, T., Yoshikawa, S.

(2009) Proc Natl Acad Sci U S A 106: 2165-2169

Released	2010-01-19
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PER, PGV, PSC, TGL, UNX, ZN

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3J6H \| pdb_00003j6h	Download File View File

Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule

Morikawa, M., Yajima, H., Nitta, R., Inoue, S., Ogura, T., Sato, C., Hirokawa, N.

(2015) EMBO J

Released	2015-04-01
Method	ELECTRON MICROSCOPY 8.1 Å
Organisms	Mus musculus Sus scrofa
Macromolecule	Kinesin heavy chain isoform 5C (protein) Tubulin alpha-1A chain (protein) Tubulin beta chain (protein)
Unique Ligands	G2P, GTP, MG, SO4

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3J7I \| pdb_00003j7i	Download File View File

Structure of alpha- and beta- tubulin in GMPCPP-microtubules

Yajima, H., Ogura, T., Nitta, R., Okada, Y., Sato, C., Hirokawa, N.

(2012) J Cell Biol 198: 315-322

Released	2014-12-10
Method	ELECTRON MICROSCOPY 8.9 Å
Organisms	Sus scrofa
Macromolecule	Tubulin alpha-1A chain (protein) Tubulin beta chain (protein)
Unique Ligands	GTP, MG

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3WG7 \| pdb_00003wg7	Download File View File

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E., Tono, K., Ueno, G., Hikima, T., Murakami, H., Inubushi, Y., Yabashi, M., Ishikawa, T., Yamamoto, M., Ogura, T., Sugimoto, H., Shen, J.R., Yoshikawa, S., Ago, H.

(2014) Nat Methods 11: 734-736

Released	2014-04-30
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PER, PGV, PSC, TGL, ZN

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5X19 \| pdb_00005x19	Download File View File

CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center

Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.

(2017) Sci Adv 3: e1603042-e1603042

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CMO, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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5X1B \| pdb_00005x1b	Download File View File

CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center

(2017) Sci Adv 3: e1603042-e1603042

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CMO, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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5X1F \| pdb_00005x1f	Download File View File

CO bound cytochrome c oxidase without pump laser irradiation at 278K

(2017) Sci Adv 3: e1603042-e1603042

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CMO, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PSC, TGL, UNX, ZN

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5XEC \| pdb_00005xec	Download File View File

Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins

Zhang, M., Nakanishi, T., Yamanaka, M., Nagao, S., Yanagisawa, S., Shomura, Y., Shibata, N., Ogura, T., Higuchi, Y., Hirota, S.

(2017) Chembiochem 18: 1712-1715

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Hydrogenobacter thermophilus TK-6 Pseudomonas aeruginosa PAO1
Macromolecule	Cytochrome c-551,Cytochrome c-552 (protein) Cytochrome c-552,Cytochrome c-551 (protein)
Unique Ligands	HEC

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5XED \| pdb_00005xed	Download File View File

Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins

Zhang, M., Nakanishi, T., Yamanaka, M., Nagao, S., Yanagisawa, S., Shomura, Y., Shibata, N., Ogura, T., Higuchi, Y., Hirota, S.

(2017) Chembiochem 18: 1712-1715

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Hydrogenobacter thermophilus TK-6 Pseudomonas aeruginosa PAO1
Macromolecule	Cytochrome c-551,Cytochrome c-552 (protein) Cytochrome c-552,Cytochrome c-551 (protein)
Unique Ligands	HEC

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7CG3 \| pdb_00007cg3	Download File View File

Staggered ring conformation of CtHsp104 (Hsp104 from Chaetomium Thermophilum)

Inoue, Y., Hanazono, Y., Noi, K., Kawamoto, A., Kimatsuka, M., Harada, R., Takeda, K., Iwamasa, N., Shibata, K., Noguchi, K., Shigeta, Y., Namba, K., Ogura, T., Miki, K., Shinohara, K., Yohda, M.

(2021) Structure 29: 721-730.e6

Released	2021-04-28
Method	ELECTRON MICROSCOPY 5.1 Å
Organisms	Thermochaetoides thermophila
Macromolecule	Heat shock protein 104 (protein)

1 to 13 of 13 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1LV7 | pdb_00001lv7

Crystal Structure of the AAA domain of FtsH

2ZXW | pdb_00002zxw

Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset)

3ABL | pdb_00003abl

Bovine heart cytochrome c oxidase at the fully oxidized state (15-s X-ray exposure dataset)

3ABM | pdb_00003abm

Bovine heart cytochrome c oxidase at the fully oxidized state (200-s X-ray exposure dataset)

3J6H | pdb_00003j6h

Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule

3J7I | pdb_00003j7i

Structure of alpha- and beta- tubulin in GMPCPP-microtubules

3WG7 | pdb_00003wg7

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

5X19 | pdb_00005x19

CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center

5X1B | pdb_00005x1b

CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center

5X1F | pdb_00005x1f

CO bound cytochrome c oxidase without pump laser irradiation at 278K

5XEC | pdb_00005xec

Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins

5XED | pdb_00005xed

Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins

7CG3 | pdb_00007cg3

Staggered ring conformation of CtHsp104 (Hsp104 from Chaetomium Thermophilum)

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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

1LV7 | pdb_00001lv7

2ZXW | pdb_00002zxw

3ABL | pdb_00003abl

3ABM | pdb_00003abm

3J6H | pdb_00003j6h

3J7I | pdb_00003j7i

3WG7 | pdb_00003wg7

5X19 | pdb_00005x19

5X1B | pdb_00005x1b

5X1F | pdb_00005x1f

5XEC | pdb_00005xec

5XED | pdb_00005xed

7CG3 | pdb_00007cg3