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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Harada, R."

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Search Summary

This query matches 9 Structures.

Refinements

Structure Determination Methodology

experimental (9)

Scientific Name of Source Organism

	Staphylococcus aureus subsp. aureus MRSA252 (3)
	Bos taurus (2)
	Escherichia coli (2)
	Thermochaetoides thermophila (2)

Taxonomy

	Bacteria (5)
	Eukaryota (4)

Experimental Method

	X-RAY DIFFRACTION (6)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (9)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (3)
	2.5 - 3.0 (2)
	3.0 - 3.5 (1)
	> 4.5 (1)

Release Date

	2015 - 2019 (4)
	2020 - 2024 (5)

Enzyme Classification Name

Translocases (4)

Membrane Protein Annotation

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

Symmetry Type

	Asymmetric (7)
	Helical (2)

SCOP Classification

	Alpha and beta proteins (a/b) (4)
	Alpha and beta proteins (a+b) (3)
	Artifacts (3)

AllSelected

1 to 9 of 9 Structures

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5H5G \| pdb_00005h5g	Download File View File

Staphylococcus aureus FtsZ-GDP in T and R states

Fujita, J., Harada, R., Maeda, Y., Saito, Y., Mizohata, E., Inoue, T., Shigeta, Y., Matsumura, H.

(2017) J Struct Biol 198: 65-73

Released	2017-05-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Staphylococcus aureus subsp. aureus MRSA252
Macromolecule	Cell division protein FtsZ (protein)
Unique Ligands	CA, GDP

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5H5H \| pdb_00005h5h	Download File View File

Staphylococcus aureus FtsZ-GDP R29A mutant in T state

Fujita, J., Harada, R., Maeda, Y., Saito, Y., Mizohata, E., Inoue, T., Shigeta, Y., Matsumura, H.

(2017) J Struct Biol 198: 65-73

Released	2017-05-24
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Staphylococcus aureus subsp. aureus MRSA252
Macromolecule	Cell division protein FtsZ (protein)
Unique Ligands	CA, GDP

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5H5I \| pdb_00005h5i	Download File View File

Staphylococcus aureus FtsZ-GDP R29A mutant in R state

Fujita, J., Harada, R., Maeda, Y., Saito, Y., Mizohata, E., Inoue, T., Shigeta, Y., Matsumura, H.

(2017) J Struct Biol 198: 65-73

Released	2017-05-24
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Staphylococcus aureus subsp. aureus MRSA252
Macromolecule	Cell division protein FtsZ (protein)
Unique Ligands	GDP

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5ZUI \| pdb_00005zui	Download File View File

Crystal Structure of HSP104 from Chaetomium thermophilum

Hanazono, Y., Inoue, Y., Noguchi, K., Yohda, M., Shinohara, K., Takeda, K., Miki, K.

(2021) Structure

Released	2019-06-19
Method	X-RAY DIFFRACTION 2.701 Å
Organisms	Thermochaetoides thermophila
Macromolecule	Heat Shock Protein 104 (protein)
Unique Ligands	ADP, SO4

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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)

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7XMA \| pdb_00007xma	Download File View File

Crystal structure of Bovine heart cytochrome c oxidase, apo structure with DMSO

Nishida, Y., Shinzawa-Itoh, K., Mizuno, N., Kumasaka, T., Yoshikawa, S., Tsukihara, T., Takashima, S., Shintani, Y.

(2022) Nat Commun 13: 7591-7591

Released	2022-12-21
Method	X-RAY DIFFRACTION 2.2 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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7XMB \| pdb_00007xmb	Download File View File

Crystal structure of Bovine heart cytochrome c oxidase, the structure complexed with an allosteric inhibitor T113

Nishida, Y., Shinzawa-Itoh, K., Mizuno, N., Kumasaka, T., Yoshikawa, S., Tsukihara, T., Shintani, Y., Takashima, S.

(2022) Nat Commun 13: 7591-7591

Released	2022-12-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, J6X, MG, NA, PEK, PER, PGV, PSC, TGL, ZN

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7XMC \| pdb_00007xmc	Download File View File

Cryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO

Nishida, Y., Shigematsu, H., Iwamoto, T., Takashima, S., Shintani, Y.

(2022) Nat Commun 13: 7591-7591

Released	2022-12-21
Method	ELECTRON MICROSCOPY 3.09 Å
Organisms	Escherichia coli
Macromolecule	Cytochrome bo(3) ubiquinol oxidase subunit 1 (protein) Cytochrome bo(3) ubiquinol oxidase subunit 3 (protein) Cytochrome bo(3) ubiquinol oxidase subunit 4 (protein) Ubiquinol oxidase subunit 2 (protein)
Unique Ligands	CU, HEM, HEO, PEE, UNX

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7XMD \| pdb_00007xmd	Download File View File

Cryo-EM structure of Cytochrome bo3 from Escherichia coli, the structure complexed with an allosteric inhibitor N4

Nishida, Y., Shigematsu, H., Iwamoto, T., Takashima, S., Shintani, Y.

(2022) Nat Commun 13: 7591-7591

Released	2022-12-21
Method	ELECTRON MICROSCOPY 2.99 Å
Organisms	Escherichia coli
Macromolecule	Cytochrome bo(3) ubiquinol oxidase subunit 1 (protein) Cytochrome bo(3) ubiquinol oxidase subunit 3 (protein) Cytochrome bo(3) ubiquinol oxidase subunit 4 (protein) Ubiquinol oxidase subunit 2 (protein)
Unique Ligands	CU, HEM, HEO, JYR, PEE, UNX

1 to 9 of 9 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.

5H5G | pdb_00005h5g

Staphylococcus aureus FtsZ-GDP in T and R states

5H5H | pdb_00005h5h

Staphylococcus aureus FtsZ-GDP R29A mutant in T state

5H5I | pdb_00005h5i

Staphylococcus aureus FtsZ-GDP R29A mutant in R state

5ZUI | pdb_00005zui

Crystal Structure of HSP104 from Chaetomium thermophilum

7CG3 | pdb_00007cg3

Staggered ring conformation of CtHsp104 (Hsp104 from Chaetomium Thermophilum)

7XMA | pdb_00007xma

Crystal structure of Bovine heart cytochrome c oxidase, apo structure with DMSO

7XMB | pdb_00007xmb

Crystal structure of Bovine heart cytochrome c oxidase, the structure complexed with an allosteric inhibitor T113

7XMC | pdb_00007xmc

Cryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO

7XMD | pdb_00007xmd

Cryo-EM structure of Cytochrome bo3 from Escherichia coli, the structure complexed with an allosteric inhibitor N4

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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

5H5G | pdb_00005h5g

5H5H | pdb_00005h5h

5H5I | pdb_00005h5i

5ZUI | pdb_00005zui

7CG3 | pdb_00007cg3

7XMA | pdb_00007xma

7XMB | pdb_00007xmb

7XMC | pdb_00007xmc

7XMD | pdb_00007xmd