RCSB PDB: Search

3WO6 \| pdb_00003wo6	Download File View File

Crystal structure of YidC from Bacillus halodurans (form I)

Kumazaki, K., Tsukazaki, T., Ishitani, R., Nureki, O.

(2014) Nature 509: 516-520

Released	2014-04-23
Method	X-RAY DIFFRACTION 2.403 Å
Organisms	Halalkalibacterium halodurans C-125
Macromolecule	Membrane protein insertase YidC 2 (protein)
Unique Ligands	CD, OLC

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3WO7 \| pdb_00003wo7	Download File View File

Crystal structure of YidC from Bacillus halodurans (form II)

Kumazaki, K., Tsukazaki, T., Ishitani, R., Nureki, O.

(2014) Nature 509: 516-520

Released	2014-04-23
Method	X-RAY DIFFRACTION 3.201 Å
Organisms	Halalkalibacterium halodurans C-125
Macromolecule	Membrane protein insertase YidC 2 (protein)
Unique Ligands	CU

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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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5AWW \| pdb_00005aww	Download File View File

Precise Resting State of Thermus thermophilus SecYEG

Tanaka, Y., Sugano, Y., Takemoto, M., Kusakizako, T., Kumazaki, K., Ishitani, R., Nureki, O., Tsukazaki, T.

(2015) Cell Rep 13: 1561-1568

Released	2015-11-25
Method	X-RAY DIFFRACTION 2.724 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Protein translocase subunit SecE (protein) Protein translocase subunit SecY (protein) Putative preprotein translocase, SecG subunit (protein)
Unique Ligands	OLC

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5CH4 \| pdb_00005ch4	Download File View File

Peptide-Bound State of Thermus thermophilus SecYEG

Tanaka, Y., Sugano, Y., Takemoto, M., Kusakizako, T., Kumazaki, K., Ishitani, R., Nureki, O., Tsukazaki, T.

(2015) Cell Rep 13: 1561-1568

Released	2015-11-25
Method	X-RAY DIFFRACTION 3.64 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Protein translocase subunit SecE (protein) Protein translocase subunit SecY (protein) Putative preprotein translocase, SecG subunit (protein)

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5F1C \| pdb_00005f1c	Download File View File

Crystal structure of an invertebrate P2X receptor from the Gulf Coast tick in the presence of ATP and Zn2+ ion at 2.9 Angstroms

Kasuya, G., Hattori, M., Ishitani, R., Nureki, O.

(2016) Cell Rep 14: 932-944

Released	2016-03-16
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Amblyomma maculatum
Macromolecule	Putative uncharacterized protein (protein)
Unique Ligands	ATP, NAG, ZN

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5H35 \| pdb_00005h35	Download File View File

Crystal structures of the TRIC trimeric intracellular cation channel orthologue from Sulfolobus solfataricus

Kasuya, G., Hiraizumi, M., Hattori, M., Nureki, O.

(2016) Cell Res 26: 1288-1301

Released	2017-01-11
Method	X-RAY DIFFRACTION 2.642 Å
Organisms	Mus musculus Saccharolobus solfataricus
Macromolecule	Fab Heavy Chain (protein) Fab Light Chain (protein) Membrane protein TRIC (protein)
Unique Ligands	GOL, NA, PX4

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5H36 \| pdb_00005h36	Download File View File

Crystal structures of the TRIC trimeric intracellular cation channel orthologue from Rhodobacter sphaeroides

Kasuya, G., Hiraizumi, M., Hattori, M., Nureki, O.

(2016) Cell Res 26: 1288-1301

Released	2017-01-11
Method	X-RAY DIFFRACTION 3.409 Å
Organisms	Cereibacter sphaeroides 2.4.1
Macromolecule	Uncharacterized protein TRIC (protein)
Unique Ligands	PX4

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5I20 \| pdb_00005i20	Download File View File

Crystal structure of protein

Ishitani, R., Nureki, O.

(2016) Nature 534: 417-420

Released	2016-06-01
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Ancylobacter novellus DSM 506
Macromolecule	Uncharacterized protein (protein)
Unique Ligands	OLC, SO4

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5XW6 \| pdb_00005xw6	Download File View File

Crystal structure of the chicken ATP-gated P2X7 receptor channel in the presence of competitive antagonist TNP-ATP at 3.1 Angstroms

Kasuya, G., Hattori, M., Nureki, O.

(2017) Nat Commun 8: 876-876

Released	2017-10-25
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Gallus gallus
Macromolecule	P2X purinoceptor (protein)
Unique Ligands	128, NAG

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5Y4H \| pdb_00005y4h	Download File View File

Human SIRT3 in complex with halistanol sulfate

Kudo, N., Ito, A., Yoshida, M.

(2018) J Antibiot (Tokyo) 71: 273-278

Released	2018-05-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacetylase sirtuin-3, mitochondrial (protein) THr-Arg-Ser-GLY-ALY-VAL-MET-ARG-ARG-LEU-ARG-ARG (protein)
Unique Ligands	8QF, ZN

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5Y78 \| pdb_00005y78	Download File View File

Crystal structure of the triose-phosphate/phosphate translocator in complex with inorganic phosphate

Lee, Y., Nishizawa, T., Takemoto, M., Kumazaki, K., Yamashita, K., Hirata, K., Minoda, A., Nagatoishi, S., Tsumoto, K., Ishitani, R., Nureki, O.

(2017) Nat Plants 3: 825-832

Released	2017-10-04
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Galdieria sulphuraria
Macromolecule	Putative hexose phosphate translocator (protein)
Unique Ligands	OLC, PO4

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5Y79 \| pdb_00005y79	Download File View File

Crystal structure of the triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate

Lee, Y., Nishizawa, T., Takemoto, M., Kumazaki, K., Yamashita, K., Hirata, K., Minoda, A., Nagatoishi, S., Tsumoto, K., Ishitani, R., Nureki, O.

(2017) Nat Plants 3: 825-832

Released	2017-10-04
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Galdieria sulphuraria
Macromolecule	Putative hexose phosphate translocator (protein)
Unique Ligands	3PG, FLC, OLC

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6K4J \| pdb_00006k4j	Download File View File

Crystal Structure of the the CD9

Umeda, R., Nishizawa, T., Sato, K., Nureki, O.

(2020) Nat Commun 11: 1606-1606

Released	2020-05-13
Method	X-RAY DIFFRACTION 2.701 Å
Organisms	Homo sapiens
Macromolecule	CD9 antigen (protein)
Unique Ligands	NI, OLC, PLM

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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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7CCS \| pdb_00007ccs	Download File View File

Consensus mutated xCT-CD98hc complex

Oda, K., Lee, Y., Takemoto, M., Yamashita, K., Nishizawa, T., Nureki, O.

(2020) Protein Sci 29: 2398-2407

Released	2020-12-09
Method	ELECTRON MICROSCOPY 6.2 Å
Organisms	Homo sapiens
Macromolecule	4F2 cell-surface antigen heavy chain (protein) Consensus mutated Anionic Amino Acid Transporter Light Chain, Xc- System (protein)

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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

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7W6X \| pdb_00007w6x	Download File View File

Crystal structure of E. coli RseP in complex with batimastat

Takanuki, K., Imaizumi, Y., Nogi, T.

(2022) Sci Adv 8: eabp9011-eabp9011

Released	2022-09-07
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Escherichia coli K-12
Macromolecule	Regulator of sigma-E protease RseP (protein)
Unique Ligands	BAT, ZN

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7W6Y \| pdb_00007w6y	Download File View File

Crystal structure of Kangiella koreensis RseP orthologue in complex with batimastat in space group P1

Imaizumi, Y., Takanuki, K., Nogi, T.

(2022) Sci Adv 8: eabp9011-eabp9011

Released	2022-09-07
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Kangiella koreensis DSM 16069
Macromolecule	Anti sigma-E protein, RseA (protein)
Unique Ligands	BAT, ZN

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7W6Z \| pdb_00007w6z	Download File View File

Crystal structure of Kangiella koreensis RseP orthologue in complex with batimastat in space group P21

Imaizumi, Y., Takanuki, K., Nogi, T.

(2022) Sci Adv 8: eabp9011-eabp9011

Released	2022-09-07
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Kangiella koreensis DSM 16069
Macromolecule	Zinc metalloprotease (protein)
Unique Ligands	BAT, ZN

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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

3WO6 | pdb_00003wo6

3WO7 | pdb_00003wo7

3X3B | pdb_00003x3b

3X3C | pdb_00003x3c

5AWW | pdb_00005aww

5CH4 | pdb_00005ch4

5F1C | pdb_00005f1c

5H35 | pdb_00005h35

5H36 | pdb_00005h36

5I20 | pdb_00005i20

5XW6 | pdb_00005xw6

5Y4H | pdb_00005y4h

5Y78 | pdb_00005y78

5Y79 | pdb_00005y79

6K4J | pdb_00006k4j

7C86 | pdb_00007c86

7CCS | pdb_00007ccs

7E6X | pdb_00007e6x

7E6Y | pdb_00007e6y

7E6Z | pdb_00007e6z

7E70 | pdb_00007e70

7E71 | pdb_00007e71

7W6X | pdb_00007w6x

7W6Y | pdb_00007w6y

7W6Z | pdb_00007w6z