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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ohki, M."

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Search Summary

This query matches 65 Structures.

Refinements

Structure Determination Methodology

experimental (65)

Scientific Name of Source Organism

	Homo sapiens (33)
	Nonlabens marinus S1-08 (21)
	Mus musculus (5)
	Cyanobacteriota (3)
	Mastigocladopsis repens (3)
	Oscillatoria acuminata PCC 6304 (2)
	Influenza A virus (A/Puerto Rico/8/1934(H1N1)) (1)
	Nonlabens marinus (1)
	Saccharomyces cerevisiae S288C (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (34)
	Bacteria (30)
	Riboviria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (56)
	ELECTRON MICROSCOPY (9)

Polymer Entity Type

Protein (65)

Refinement Resolution (Å)

	1.0 - 1.5 (11)
	1.5 - 2.0 (34)
	2.0 - 2.5 (5)
	2.5 - 3.0 (7)
	3.0 - 3.5 (7)
	3.5 - 4.0 (1)

Release Date

	2010 - 2014 (1)
	2015 - 2019 (14)
	2020 - 2024 (50)

Enzyme Classification Name

	Hydrolases (4)
	Lyases (2)
	Transferases (1)

Membrane Protein Annotation

	PDBTM (33)
	mpstruc (28)
	MemProtMD (27)
	OPM (4)

Symmetry Type

	Cyclic (33)
	Asymmetric (32)

SCOP Classification

	All alpha proteins (22)
	Alpha and beta proteins (a+b) (1)
	Membrane and cell surface proteins and peptides (25)

AllSelected

1 to 25 of 65 Structures

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4EU2 \| pdb_00004eu2	Download File View File

Crystal structure of 20s proteasome with novel inhibitor K-7174

Kikuchi, J., Shibayama, N., Yamada, S., Wada, T., Nobuyoshi, M., Izumi, T., Akutsu, M., Kano, Y., Ohki, M., Sugiyama, K., Park, S.-Y., Furukawa, Y.

(2013) PLoS One 8: e60649-e60649

Released	2013-05-01
Method	X-RAY DIFFRACTION 2.509 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 14
Unique Ligands	WPI

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4YUS \| pdb_00004yus	Download File View File

Crystal structure of photoactivated adenylyl cyclase of a cyanobacteriaOscillatoria acuminata in hexagonal form

Park, S.-Y., Ohki, M., Sugiyama, K., Kawai, F., Iseki, M.

(2016) Proc Natl Acad Sci U S A 113: 6659-6664

Released	2016-06-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Oscillatoria acuminata PCC 6304
Macromolecule	Family 3 adenylate cyclase (protein)
Unique Ligands	FMN

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4YUT \| pdb_00004yut	Download File View File

Crystal structure of photoactivated adenylyl cyclase of a cyanobacteriaOscillatoria acuminata in orthorhombic form

Park, S.-Y., Ohki, M., Sugiyama, K., Kawai, F., Iseki, M.

(2016) Proc Natl Acad Sci U S A 113: 6659-6664

Released	2016-06-01
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Oscillatoria acuminata PCC 6304
Macromolecule	Family 3 adenylate cyclase (protein)
Unique Ligands	FMN

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5X2R \| pdb_00005x2r	Download File View File

Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 10 mM phosphate pH 6.9.

Ohki, M., Park, S.-Y.

(2017) J Biological Chem 292: 18258-18269

Released	2017-09-20
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin subunit alpha (protein) Hemoglobin subunit beta (protein)
Unique Ligands	HEM, HNI

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5X2S \| pdb_00005x2s	Download File View File

Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 4 mM bezafibrate pH 6.5.

Ohki, M., Park, S.-Y.

(2017) J Biological Chem 292: 18258-18269

Released	2017-09-27
Method	X-RAY DIFFRACTION 2.39 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin subunit alpha (protein) Hemoglobin subunit beta (protein)
Unique Ligands	HEM, HNI, PEM

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5X2T \| pdb_00005x2t	Download File View File

Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 4 mM bezafibrate pH 7.2.

Ohki, M., Park, S.-Y.

(2017) J Biological Chem 292: 18258-18269

Released	2017-09-20
Method	X-RAY DIFFRACTION 2.64 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin subunit alpha (protein) Hemoglobin subunit beta (protein)
Unique Ligands	HEM, HNI, PEM

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5X2U \| pdb_00005x2u	Download File View File

Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 80 mM phosphate pH 6.7.

Ohki, M., Park, S.-Y.

(2017) J Biological Chem 292: 18258-18269

Released	2017-09-27
Method	X-RAY DIFFRACTION 2.53 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin subunit alpha (protein) Hemoglobin subunit beta (protein)
Unique Ligands	HEM, HNI

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5X4T \| pdb_00005x4t	Download File View File

PAC from Oscillatoria acuminata after 20 seconds photoactivation

Ohki, M., Park, S.-Y.

(2017) Proc Natl Acad Sci U S A 114: 8562-8567

Released	2017-07-26
Method	X-RAY DIFFRACTION 1.601 Å
Organisms	Cyanobacteriota
Macromolecule	Photoactivated adenylyl cyclase (protein)
Unique Ligands	FMN

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5X4U \| pdb_00005x4u	Download File View File

PAC from Oscillatoriaacuminata after 60 seconds photoactivation

Ohki, M., Park, S.-Y.

(2017) Proc Natl Acad Sci U S A 114: 8562-8567

Released	2017-07-26
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Cyanobacteriota
Macromolecule	Photoactivated adenylyl cyclase (protein)
Unique Ligands	FMN

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5X4V \| pdb_00005x4v	Download File View File

Roseoflavin substituted OaPAC

Ohki, M., Park, S.-Y.

(2017) Proc Natl Acad Sci U S A 114: 8562-8567

Released	2017-07-26
Method	X-RAY DIFFRACTION 2 Å
Organisms	Cyanobacteriota
Macromolecule	Photoactivated adenylyl cyclase (protein)
Unique Ligands	RS3

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5XG5 \| pdb_00005xg5	Download File View File

Crystal structure of Mitsuba-1 with bound NAcGal

Terada, D., Voet, A.R.D., Kamata, K., Zhang, K.Y.J., Tame, J.R.H.

(2017) Sci Rep 7: 5943-5943

Released	2017-07-12
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	synthetic construct
Macromolecule	MITSUBA-1 (protein)
Unique Ligands	A2G

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5ZTK \| pdb_00005ztk	Download File View File

Synchrotron structure of light-driven chloride pump having an NTQ motif

Yun, J.H., Park, J.H., Park, S.Y., Lee, W.

(2019) J Biological Chem 294: 794-804

Released	2018-12-05
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

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5ZTL \| pdb_00005ztl	Download File View File

Non-cryogenic structure of light-driven chloride pump having an NTQ motif

Yun, J.H., Park, S.Y., Liu, H., Lee, W.

(2019) J Biological Chem 294: 794-804

Released	2018-12-05
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Nonlabens marinus
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

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6AB9 \| pdb_00006ab9	Download File View File

The crystal structure of the relaxed state of Nonlabens marinus Rhodopsin 3

Yun, J.-H., Ohki, M., Park, J.-H., Jin, Z., Lee, W., Liu, H., Tame, J.R.H., Shibayama, N., Park, S.-Y.

To be published

Released	2019-07-31
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

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6ABA \| pdb_00006aba	Download File View File

The crystal structure of the photoactivated state of Nonlabens marinus Rhodopsin 3

Yun, J.-H., Ohki, M., Park, J.-H., Jin, Z., Lee, W., Liu, H., Tame, J.R.H., Shibayama, N., Park, S.-Y.

To be published

Released	2019-07-31
Method	X-RAY DIFFRACTION 1.797 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

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6JY6 \| pdb_00006jy6	Download File View File

Structure of dark-state marine bacterial chloride importer, NM-R3, with Pulse laser (ND-1%) at 95K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

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6JY7 \| pdb_00006jy7	Download File View File

Structure of light-state marine bacterial chloride importer, NM-R3, with Pulse laser (ND-1%) at 95K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

Explore in 3D

6JY8 \| pdb_00006jy8	Download File View File

Structure of dark-state marine bacterial chloride importer, NM-R3, with CW laser (ND-3%) at 95K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

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6JY9 \| pdb_00006jy9	Download File View File

Structure of light-state marine bacterial chloride importer, NM-R3, with CW laser (ND-3%) at 95K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

Explore in 3D

6JYA \| pdb_00006jya	Download File View File

Structure of dark-state marine bacterial chloride importer, NM-R3, with CW laser (ND-10%) at 95K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.803 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

Explore in 3D

6JYB \| pdb_00006jyb	Download File View File

Structure of light-state marine bacterial chloride importer, NM-R3, with CW laser (ND-10%) at 95K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.802 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

Explore in 3D

6JYC \| pdb_00006jyc	Download File View File

Structure of dark-state marine bacterial chloride importer, NM-R3, with CW laser (ND-30%) at 95K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.892 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

Explore in 3D

6JYD \| pdb_00006jyd	Download File View File

Structure of light-state marine bacterial chloride importer, NM-R3, with CW laser (ND-30%) at 95K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 2.007 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

Explore in 3D

6JYE \| pdb_00006jye	Download File View File

Structure of dark-state marine bacterial chloride importer, NM-R3, with Pulse laser (ND-1%) at 140K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

Explore in 3D

6JYF \| pdb_00006jyf	Download File View File

Structure of light-state marine bacterial chloride importer, NM-R3, with Pulse laser (ND-1%) at 140K.

Yun, J.H., Ohki, M., Park, S.Y., Lee, W.

(2020) Sci Adv 6: eaay2042-eaay2042

Released	2020-03-04
Method	X-RAY DIFFRACTION 2.004 Å
Organisms	Nonlabens marinus S1-08
Macromolecule	Chloride pumping rhodopsin (protein)
Unique Ligands	CL, OLA, RET

1 to 25 of 65 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

4EU2 | pdb_00004eu2

4YUS | pdb_00004yus

4YUT | pdb_00004yut

5X2R | pdb_00005x2r

5X2S | pdb_00005x2s

5X2T | pdb_00005x2t

5X2U | pdb_00005x2u

5X4T | pdb_00005x4t

5X4U | pdb_00005x4u

5X4V | pdb_00005x4v

5XG5 | pdb_00005xg5

5ZTK | pdb_00005ztk

5ZTL | pdb_00005ztl

6AB9 | pdb_00006ab9

6ABA | pdb_00006aba

6JY6 | pdb_00006jy6

6JY7 | pdb_00006jy7

6JY8 | pdb_00006jy8

6JY9 | pdb_00006jy9

6JYA | pdb_00006jya

6JYB | pdb_00006jyb

6JYC | pdb_00006jyc

6JYD | pdb_00006jyd

6JYE | pdb_00006jye

6JYF | pdb_00006jyf