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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Hosaka, T."

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Search Summary

This query matches 66 Structures.

Refinements

Structure Determination Methodology

experimental (66)

Scientific Name of Source Organism

	Halobacterium salinarum NRC-1 (14)
	Homo sapiens (12)
	Nonlabens marinus S1-08 (4)
	Thermocrispum sp. RD004668 (4)
	Acetabularia acetabulum (3)
	Enterococcus faecium (3)
	Escherichia coli (3)
	Mus musculus (3)
	Nemophila menziesii (3)
	Pyrococcus horikoshii OT3 (3)

More...

Taxonomy

	Eukaryota (26)
	Bacteria (22)
	Archaea (20)
	Riboviria (2)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (65)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (66)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (13)
	2.0 - 2.5 (29)
	2.5 - 3.0 (17)
	3.0 - 3.5 (4)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (7)
	2010 - 2014 (1)
	2015 - 2019 (29)
	2020 - 2024 (27)

Enzyme Classification Name

	Transferases (11)
	Hydrolases (10)
	Ligases (1)
	Lyases (1)

Membrane Protein Annotation

	PDBTM (31)
	MemProtMD (30)
	mpstruc (23)
	OPM (8)

Symmetry Type

	Asymmetric (34)
	Cyclic (31)
	Dihedral (1)
	Icosahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (6)
	Membrane and cell surface proteins and peptides (19)
	All alpha proteins (5)
	Alpha and beta proteins (a/b) (4)
	Multi-domain proteins (alpha and beta) (2)
	Artifacts (2)

AllSelected

1 to 25 of 66 Structures

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1IYX \| pdb_00001iyx	Download File View File

Crystal structure of enolase from Enterococcus hirae

Hosaka, T., Meguro, T., Yamato, I., Shirakihara, Y.

(2003) J Biochem 133: 817-823

Released	2003-07-29
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Enterococcus hirae
Macromolecule	ENOLASE (protein)
Unique Ligands	GOL, MG, SO4

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1SMY \| pdb_00001smy	Download File View File

Structural basis for transcription regulation by alarmone ppGpp

Artsimovitch, I., Patlan, V., Sekine, S., Vassylyeva, M.N., Hosaka, T., Ochi, K., Yokoyama, S., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Cell 117: 299-310

Released	2004-05-18
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermus thermophilus
Macromolecule	DNA-directed RNA polymerase alpha chain (protein) DNA-directed RNA polymerase beta chain (protein) DNA-directed RNA polymerase beta' chain (protein) RNA POLYMERASE OMEGA SUBUNIT (protein) principal sigma factor (protein)
Unique Ligands	G4P, MG, ZN

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2CY9 \| pdb_00002cy9	Download File View File

Crystal structure of thioesterase superfamily member2 from Mus musculus

Hosaka, T., Murayama, K., Kishishita, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2006-01-06
Method	X-RAY DIFFRACTION 2.72 Å
Organisms	Mus musculus
Macromolecule	Thioesterase superfamily member 2 (protein)

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2CYE \| pdb_00002cye	Download File View File

Crystal structure of Thioesterase complexed with coenzyme A and Zn from Thermus thermophilus HB8

Hosaka, T., Kato-Murayama, M., Murayama, K., Kishishita, S., Handa, N., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Acta Crystallogr D Biol Crystallogr 65: 767-776

Released	2006-01-06
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Putative thioesterase (protein)
Unique Ligands	COA, ZN

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2DBB \| pdb_00002dbb	Download File View File

Crystal structure of PH0061

Nishino, A., Hosaka, T., Murayama, K., Shirouzu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2006-06-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Putative HTH-type transcriptional regulator PH0061 (protein)

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2DUK \| pdb_00002duk	Download File View File

Crystal structure of MS0616

Hosaka, T., Nishino, A., Uchikubo, K.-T., Kishishita, S., Murayama, K., Shirouzu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-01-24
Method	X-RAY DIFFRACTION 2.62 Å
Organisms	Mus musculus
Macromolecule	MS0616 (protein)

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2DUM \| pdb_00002dum	Download File View File

Crystal structure of hypothetical protein, PH0823

Hosaka, T., Kishishita, S., Murayama, K., Shirouzu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-01-24
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Hypothetical protein PH0823 (protein)

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2EJ8 \| pdb_00002ej8	Download File View File

Crystal structure of APPL1 PTB domain at 1.8A

Tanabe, H., Hosaka, T., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Homo sapiens
Macromolecule	DCC-interacting protein 13 alpha (protein)

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2YX6 \| pdb_00002yx6	Download File View File

Crystal structure of PH0822

Hosaka, T., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-10-30
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Hypothetical protein PH0822 (protein)
Unique Ligands	ADP

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3VTA \| pdb_00003vta	Download File View File

Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L

Murayama, K., Kato-Murayama, M., Hosaka, T., Sotokawauchi, A., Shirouzu, M., Arima, K., Yokoyama, S.

(2012) J Mol Biology 423: 386-396

Released	2012-08-08
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Cucumis melo
Macromolecule	Cucumisin (protein)
Unique Ligands	DFP
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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3WPQ \| pdb_00003wpq	Download File View File

crystal structure of the GAP domain of MgcRacGAP(S387A)

Murayama, K., Kato-Murayama, M., Shirouzu, M., Kitamura, T., Yokoyama, S.

(2024) J Struct Biol 216: 108151-108151

Released	2015-01-21
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Homo sapiens
Macromolecule	Rac GTPase-activating protein 1 (protein)

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3WPS \| pdb_00003wps	Download File View File

crystal structure of the GAP domain of MgcRacGAP(S387D)

Murayama, K., Kato-murayama, M., Shirouzu, M., Kitamura, T., Yokoyama, S.

(2024) J Struct Biol 216: 108151-108151

Released	2015-01-21
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Rac GTPase-activating protein 1 (protein)
Unique Ligands	SO4

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4YN3 \| pdb_00004yn3	Download File View File

Crystal structure of Cucumisin complex with pro-peptide

Murayama, K., Kato-Murayama, M., Yokoyama, S., Arima, K., Shirouzu, M.

(2017) J Biochem 161: 45-53

Released	2016-03-09
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Cucumis melo
Macromolecule	Cucumisin (protein)
Unique Ligands	CL, GOL, PEG
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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5AWZ \| pdb_00005awz	Download File View File

Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.57 angstrom

Furuse, M., Hosaka, T., Kimura-Someya, T., Yokoyama, S., Shirouzu, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2203-2216

Released	2015-08-26
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Acetabularia acetabulum
Macromolecule	Rhodopsin I (protein)
Unique Ligands	C14, D10, D12, OCT, OLB, RET

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5AX0 \| pdb_00005ax0	Download File View File

Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.52 angstrom

Furuse, M., Hosaka, T., Kimura-Someya, T., Yokoyama, S., Shirouzu, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2203-2216

Released	2015-08-26
Method	X-RAY DIFFRACTION 1.521 Å
Organisms	Acetabularia acetabulum
Macromolecule	Rhodopsin I (protein)
Unique Ligands	C14, D10, D12, OLB, R16, RET

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5AX1 \| pdb_00005ax1	Download File View File

Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.80 angstrom

Furuse, M., Hosaka, T., Kimura-Someya, T., Yokoyama, S., Shirouzu, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2203-2216

Released	2015-08-26
Method	X-RAY DIFFRACTION 1.803 Å
Organisms	Acetabularia acetabulum
Macromolecule	Rhodopsin I (protein)
Unique Ligands	C14, D10, D12, OLB, R16, RET

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5B2N \| pdb_00005b2n	Download File View File

Crystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus

Hosaka, T., Kimura-Someya, T., Shirouzu, M.

(2016) J Biological Chem 291: 17488-17495

Released	2016-07-13
Method	X-RAY DIFFRACTION 1.581 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, D10, D12, HEX, OCT, RET

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5B34 \| pdb_00005b34	Download File View File

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

Mizohata, E., Nakane, T.

(2016) Proc Natl Acad Sci U S A 113: 13039-13044

Released	2016-11-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	4QL, D10, D12, DD9, HP6, OCT, R16, RET

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5B35 \| pdb_00005b35	Download File View File

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

Mizohata, E., Nakane, T., Suzuki, M.

(2016) Proc Natl Acad Sci U S A 113: 13039-13044

Released	2016-11-09
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Halobacterium salinarum
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	4QM, D10, D12, DD9, HP6, OCT, R16, RET

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5B6V \| pdb_00005b6v	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: resting state structure

Nango, E., Royant, A., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5B6W \| pdb_00005b6w	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 16 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5B6X \| pdb_00005b6x	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 760 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5B6Y \| pdb_00005b6y	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 36.2 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5B6Z \| pdb_00005b6z	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 1.725 ms us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5C2J \| pdb_00005c2j	Download File View File

Complex structure of the GAP domain of MgcRacGAP and Cdc42

Murayama, K., Kato-Murayama, M., Hosaka, T., Kitamura, T., Yokoyama, S., Shirouzu, M.

(2024) J Struct Biol 216: 108151-108151

Released	2016-06-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Cell division control protein 42 homolog (protein) Rac GTPase-activating protein 1 (protein)
Unique Ligands	AF3, GDP, MG

1 to 25 of 66 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

1IYX | pdb_00001iyx

1SMY | pdb_00001smy

2CY9 | pdb_00002cy9

2CYE | pdb_00002cye

2DBB | pdb_00002dbb

2DUK | pdb_00002duk

2DUM | pdb_00002dum

2EJ8 | pdb_00002ej8

2YX6 | pdb_00002yx6

3VTA | pdb_00003vta

3WPQ | pdb_00003wpq

3WPS | pdb_00003wps

4YN3 | pdb_00004yn3

5AWZ | pdb_00005awz

5AX0 | pdb_00005ax0

5AX1 | pdb_00005ax1

5B2N | pdb_00005b2n

5B34 | pdb_00005b34

5B35 | pdb_00005b35

5B6V | pdb_00005b6v

5B6W | pdb_00005b6w

5B6X | pdb_00005b6x

5B6Y | pdb_00005b6y

5B6Z | pdb_00005b6z

5C2J | pdb_00005c2j