RCSB PDB: Search

3X3B \| pdb_00003x3b	Download File View File

Crystal structure of the light-driven sodium pump KR2 in acidic state

Kato, H.E., Inoue, K., Abe-Yoshizumi, R., Kato, Y., Ono, H., Konno, M., Ishizuka, T., Hoque, M.R., Hososhima, S., Kunitomo, H., Ito, J., Yoshizawa, S., Yamashita, K., Takemoto, M., Nishizawa, T., Taniguchi, R., Kogure, K., Maturana, A.D., Iino, Y., Yawo, H., Ishitani, R., Kandori, H., Nureki, O.

(2015) Nature 521: 48-53

Released	2015-04-08
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	OLA, PEG, RET

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3X3C \| pdb_00003x3c	Download File View File

Crystal structure of the light-driven sodium pump KR2 in neutral state

Kato, H.E., Inoue, K., Abe-Yoshizumi, R., Kato, Y., Ono, H., Konno, M., Ishizuka, T., Hoque, M.R., Hososhima, S., Kunitomo, H., Ito, J., Yoshizawa, S., Yamashita, K., Takemoto, M., Nishizawa, T., Taniguchi, R., Kogure, K., Maturana, A.D., Iino, Y., Yawo, H., Ishitani, R., Kandori, H., Nureki, O.

(2015) Nature 521: 48-53

Released	2015-04-08
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	OLA, RET

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4U4T \| pdb_00004u4t	Download File View File

Structure of a nitrate/nitrite antiporter NarK in nitrate-bound inward-open state

Fukuda, M., Takeda, H., Kato, H.E., Doki, S., Ito, K., Maturana, A.D., Ishitani, R., Nureki, O.

(2015) Nat Commun 6: 7097-7097

Released	2015-07-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli str. K-12 substr. MG1655
Macromolecule	Nitrate/nitrite transporter NarK (protein)
Unique Ligands	NO3, OLA, OLC, ZN

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4U4V \| pdb_00004u4v	Download File View File

Structure of a nitrate/nitrite antiporter NarK in apo inward-open state

Fukuda, M., Takeda, H., Kato, H.E., Doki, S., Ito, K., Maturana, A.D., Ishitani, R., Nureki, O.

(2015) Nat Commun 6: 7097-7097

Released	2015-07-15
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Escherichia coli str. K-12 substr. MG1655
Macromolecule	Nitrate/nitrite transporter NarK (protein)
Unique Ligands	NI, OLA

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4U4W \| pdb_00004u4w	Download File View File

Structure of a nitrate/nitrite antiporter NarK in nitrate-bound occluded state

Fukuda, M., Takeda, H., Kato, H.E., Doki, S., Ito, K., Maturana, A.D., Ishitani, R., Nureki, O.

(2015) Nat Commun 6: 7097-7097

Released	2015-07-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli str. K-12 substr. MG1655
Macromolecule	Nitrate/nitrite transporter NarK (protein)
Unique Ligands	NO3, OLA, OLC

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4U9L \| pdb_00004u9l	Download File View File

Structure of a membrane protein

Takeda, H., Hattori, M., Nishizawa, T., Yamashita, K., Shah, S.T.A., Caffrey, M., Maturana, A.D., Ishitani, R., Nureki, O.

(2014) Nat Commun 5: 5374-5374

Released	2014-12-03
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Magnesium transporter MgtE (protein)
Unique Ligands	MG, OLC

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4U9N \| pdb_00004u9n	Download File View File

Structure of a membrane protein

Takeda, H., Hattori, M., Nishizawa, T., Yamashita, K., Shah, S.T.A., Caffrey, M., Maturana, A.D., Ishitani, R., Nureki, O.

(2014) Nat Commun 5: 5374-5374

Released	2014-12-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Magnesium transporter MgtE (protein)
Unique Ligands	MN, OLA, OLC

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4WIB \| pdb_00004wib	Download File View File

Crystal structure of Magnesium transporter MgtE

Takeda, H., Hattori, M., Nishizawa, T., Yamashita, K., Shah, S.T.A., Caffrey, M., Maturana, A.D., Ishitani, R., Nureki, O.

(2014) Nat Commun 5: 5374-5374

Released	2014-12-03
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Magnesium transporter MgtE (protein)
Unique Ligands	CA

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6IDP \| pdb_00006idp	Download File View File

Crystal structure of Vibrio cholerae MATE transporter VcmN in the straight form

Kusakizako, T., Claxton, D.P., Tanaka, Y., Maturana, A.D., Kuroda, T., Ishitani, R., Mchaourab, H.S., Nureki, O.

(2019) Structure 27: 293

Released	2019-01-16
Method	X-RAY DIFFRACTION 2.205 Å
Organisms	Vibrio cholerae
Macromolecule	MATE family efflux transporter (protein)
Unique Ligands	OLC

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6IDR \| pdb_00006idr	Download File View File

Crystal structure of Vibrio cholerae MATE transporter VcmN in the bent form

Kusakizako, T., Claxton, D.P., Tanaka, Y., Maturana, A.D., Kuroda, T., Ishitani, R., Mchaourab, H.S., Nureki, O.

(2019) Structure 27: 293

Released	2019-01-16
Method	X-RAY DIFFRACTION 2.502 Å
Organisms	Vibrio cholerae
Macromolecule	MATE family efflux transporter (protein)
Unique Ligands	OLC

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6IDS \| pdb_00006ids	Download File View File

Crystal structure of Vibrio cholerae MATE transporter VcmN D35N mutant

Kusakizako, T., Claxton, D.P., Tanaka, Y., Maturana, A.D., Kuroda, T., Ishitani, R., Mchaourab, H.S., Nureki, O.

(2019) Structure 27: 293

Released	2019-01-16
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Vibrio cholerae
Macromolecule	MATE family efflux transporter (protein)
Unique Ligands	OLC

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7C86 \| pdb_00007c86	Download File View File

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure

Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., Nureki, O.

(2021) Elife 10:

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Sensory opsin A,Channelrhodopsin (ChR) chimera between ChR1 & ChR2 (protein)
Unique Ligands	OLC, RET
Unique branched monosaccharides	NAG

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7E6X \| pdb_00007e6x	Download File View File

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 4 ms structure

Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., Nureki, O.

(2021) Elife 10:

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Archaeal-type opsin 1,Archaeal-type opsin 2 (protein)
Unique Ligands	OLC, RET
Unique branched monosaccharides	NAG

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7E6Y \| pdb_00007e6y	Download File View File

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 microsecond structure

Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., Nureki, O.

(2021) Elife 10:

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Archaeal-type opsin 1,Archaeal-type opsin 2 (protein)
Unique Ligands	OLC, RET
Unique branched monosaccharides	NAG

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7E6Z \| pdb_00007e6z	Download File View File

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 50 microsecond structure

Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., Nureki, O.

(2021) Elife 10:

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Archaeal-type opsin 1,Archaeal-type opsin 2 (protein)
Unique Ligands	OLC, RET
Unique branched monosaccharides	NAG

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7E70 \| pdb_00007e70	Download File View File

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 250 microsecond structure

Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., Nureki, O.

(2021) Elife 10:

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Archaeal-type opsin 1,Archaeal-type opsin 2 (protein)
Unique Ligands	OLC, RET
Unique branched monosaccharides	NAG

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7E71 \| pdb_00007e71	Download File View File

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 ms structure

Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., Nureki, O.

(2021) Elife 10:

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Chlamydomonas reinhardtii
Macromolecule	Archaeal-type opsin 1,Archaeal-type opsin 2 (protein)
Unique Ligands	OLC, RET
Unique branched monosaccharides	NAG

3X3B | pdb_00003x3b

Crystal structure of the light-driven sodium pump KR2 in acidic state

3X3C | pdb_00003x3c

Crystal structure of the light-driven sodium pump KR2 in neutral state

4U4T | pdb_00004u4t

Structure of a nitrate/nitrite antiporter NarK in nitrate-bound inward-open state

4U4V | pdb_00004u4v

Structure of a nitrate/nitrite antiporter NarK in apo inward-open state

4U4W | pdb_00004u4w

Structure of a nitrate/nitrite antiporter NarK in nitrate-bound occluded state

4U9L | pdb_00004u9l

Structure of a membrane protein

4U9N | pdb_00004u9n

Structure of a membrane protein

4WIB | pdb_00004wib

Crystal structure of Magnesium transporter MgtE

6IDP | pdb_00006idp

Crystal structure of Vibrio cholerae MATE transporter VcmN in the straight form

6IDR | pdb_00006idr

Crystal structure of Vibrio cholerae MATE transporter VcmN in the bent form

6IDS | pdb_00006ids

Crystal structure of Vibrio cholerae MATE transporter VcmN D35N mutant

7C86 | pdb_00007c86

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure

7E6X | pdb_00007e6x

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 4 ms structure

7E6Y | pdb_00007e6y

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 microsecond structure

7E6Z | pdb_00007e6z

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 50 microsecond structure

7E70 | pdb_00007e70

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 250 microsecond structure

7E71 | pdb_00007e71

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 ms structure

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Membrane Protein Annotation

Symmetry Type

SCOP Classification

3X3B | pdb_00003x3b

3X3C | pdb_00003x3c

4U4T | pdb_00004u4t

4U4V | pdb_00004u4v

4U4W | pdb_00004u4w

4U9L | pdb_00004u9l

4U9N | pdb_00004u9n

4WIB | pdb_00004wib

6IDP | pdb_00006idp

6IDR | pdb_00006idr

6IDS | pdb_00006ids

7C86 | pdb_00007c86

7E6X | pdb_00007e6x

7E6Y | pdb_00007e6y

7E6Z | pdb_00007e6z

7E70 | pdb_00007e70

7E71 | pdb_00007e71