RCSB PDB: Search

5GLH	Download File View File

Human endothelin receptor type-B in complex with ET-1

Shihoya, W., Nishizawa, T., Okuta, A., Tani, K., Fujiyoshi, Y., Dohmae, N., Nureki, O., Doi, T.

(2016) Nature 537: 363-368

Released	2016-09-07
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Endothelin Receptor Subtype-B (protein) Peptide from Endothelin-1 (protein)

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5GLI	Download File View File

Human endothelin receptor type-B in the ligand-free form

Shihoya, W., Nishizawa, T., Okuta, A., Tani, K., Fujiyoshi, Y., Dohmae, N., Nureki, O., Doi, T.

(2016) Nature 537: 363-368

Released	2016-09-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Endothelin Receptor Subtype-B (protein)
Unique Ligands	OLA, OLC, SO4

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5X93	Download File View File

Human endothelin receptor type-B in complex with antagonist K-8794

Shihoya, W., Nishizawa, T., Yamashita, K., Hirata, K., Okuta, A., Tani, K., Fujiyoshi, Y., Doi, T., Nureki, O.

(2017) Nat Struct Mol Biol 24: 758-764

Released	2017-08-16
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Endothelin B receptor,Endolysin,Endothelin B receptor (protein)
Unique Ligands	CLR, K87, OLC, SO4

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5XPR	Download File View File

Human endothelin receptor type-B in complex with antagonist bosentan

Shihoya, W., Nishizawa, T., Yamashita, K., Hirata, K., Okuta, A., Tani, K., Fujiyoshi, Y., Doi, T., Nureki, O.

(2017) Nat Struct Mol Biol 24: 758-764

Released	2017-08-16
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Endothelin B receptor,Endolysin,Endothelin B receptor (protein)
Unique Ligands	K86, SO4

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6IGK	Download File View File

Crystal Structure of human ETB receptor in complex with Endothelin-3

Shihoya, W., Izume, T., Inoue, A., Yamashita, K., Kadji, F.M.N., Hirata, K., Aoki, J., Nishizawa, T., Nureki, O.

(2018) Nat Commun 9: 4711-4711

Released	2018-11-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Enterobacteria phage RB59 Homo sapiens
Macromolecule	Endothelin receptor type B,Endolysin,Endothelin receptor type B (protein) Endothelin-3 (protein)
Unique Ligands	CIT, OLC

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6IGL	Download File View File

Crystal Structure of human ETB receptor in complex with IRL1620

Shihoya, W., Izume, T., Inoue, A., Yamashita, K., kadji, F.M.N., Hirata, K., Aoki, J., Nishizawa, T., Nureki, O.

(2018) Nat Commun 9: 4711-4711

Released	2018-11-21
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Enterobacteria phage RB59 Homo sapiens
Macromolecule	Endothelin receptor type B,Endolysin,Endothelin receptor type B (protein) IRL1620 (protein)
Unique Ligands	CIT, OLC, SO4

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6IS6	Download File View File

Crystal structure of Thermoplasmatales archaeon heliorhodopsin

Shihoya, W., Yamashita, K., Nureki, O.

(2019) Nature 574: 132-136

Released	2019-09-25
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermoplasmatales archaeon SG8-52-1
Macromolecule	heliorhodopsin (protein)
Unique Ligands	OLC, RET

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6K1Q	Download File View File

Human endothelin receptor type-B in complex with inverse agonist IRL2500

Nagiri, C., Shihoya, W., Nureki, O.

(2019) Commun Biol 2: 236-236

Released	2019-07-17
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Endothelin B receptor,Endolysin,Endothelin B receptor (protein)
Unique Ligands	D2U, OLC, PO4

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6LMT	Download File View File

Cryo-EM structure of the killifish CALHM1

Demura, K., Kusakizako, T., Shihoya, W., Hiraizumi, M., Shimada, H., Yamashita, K., Nishizawa, T., Nureki, O.

(2020) Sci Adv 6: eaba8105-eaba8105

Released	2020-07-29
Method	ELECTRON MICROSCOPY 2.66 Å
Organisms	Oryzias latipes
Macromolecule	Calcium homeostasis modulator 1 (protein)
Unique Ligands	Y01

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6LMU	Download File View File

Cryo-EM structure of the human CALHM2

Demura, K., Kusakizako, T., Shihoya, W., Hiraizumi, M., Shimada, H., Yamashita, K., Nishizawa, T., Nureki, O.

(2020) Sci Adv 6: eaba8105-eaba8105

Released	2020-07-29
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens
Macromolecule	Calcium homeostasis modulator protein 2 (protein)

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6LMV	Download File View File

Cryo-EM structure of the C. elegans CLHM-1

Demura, K., Kusakizako, T., Shihoya, W., Hiraizumi, M., Shimada, H., Yamashita, K., Nishizawa, T., Nureki, O.

(2020) Sci Adv 6: eaba8105-eaba8105

Released	2020-07-29
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Caenorhabditis elegans
Macromolecule	Calcium homeostasis modulator protein (protein)

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6LMW	Download File View File

Cryo-EM structure of the CALHM chimeric construct (8-mer)

Demura, K., Kusakizako, T., Shihoya, W., Hiraizumi, M., Shimada, H., Yamashita, K., Nishizawa, T., Nureki, O.

(2020) Sci Adv 6: eaba8105-eaba8105

Released	2020-07-29
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens Oryzias latipes
Macromolecule	Calcium homeostasis modulator 1,Calcium homeostasis modulator protein 2 (protein)

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6LMX	Download File View File

Cryo-EM structure of the CALHM chimeric construct (9-mer)

Demura, K., Kusakizako, T., Shihoya, W., Hiraizumi, M., Shimada, H., Yamashita, K., Nishizawa, T., Nureki, O.

(2020) Sci Adv 6: eaba8105-eaba8105

Released	2020-07-29
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens Oryzias latipes
Macromolecule	Calcium homeostasis modulator 1,Calcium homeostasis modulator protein 2 (protein)

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6LPB	Download File View File

Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G protein

Kobayashi, K., Shihoya, W., Nishizawa, T., Nureki, O.

(2020) Nat Struct Mol Biol 27: 274-280

Released	2020-03-11
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Bos taurus Homo sapiens Rattus norvegicus unidentified
Macromolecule	Unique protein chains: 6

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6LRY	Download File View File

Crystal structure of human endothelin ETB receptor in complex with sarafotoxin S6b

Izume, T., Miyauchi, H., Shihoya, W., Nureki, O.

(2020) Biochem Biophys Res Commun 528: 383-388

Released	2020-02-12
Method	X-RAY DIFFRACTION 3 Å
Organisms	Atractaspis engaddensis Enterobacteria phage RB59 Homo sapiens
Macromolecule	Endothelin receptor type B,Endolysin,Endothelin receptor type B (protein) Sarafotoxin-B (protein)

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7C86	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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7CJ3	Download File View File

Crystal structure of the transmembrane domain of Salpingoeca rosetta rhodopsin phosphodiesterase

Ikuta, T., Shihoya, W., Yamashita, K., Nureki, O.

(2020) Nat Commun 11: 5605-5605

Released	2020-11-25
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Salpingoeca rosetta
Macromolecule	Phosphodiesterase (protein)
Unique Ligands	OLC, RET

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7CLJ	Download File View File

Crystal structure of Thermoplasmatales archaeon heliorhodopsin E108D mutant

Tanaka, T., Shihoya, W., Yamashita, K., Nureki, O.

(2020) Biochem Biophys Res Commun 533: 262-267

Released	2020-09-02
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermoplasmatales archaeon SG8-52-1
Macromolecule	heliorhodopsin (protein)
Unique Ligands	OLC, RET, SO4

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7D3S	Download File View File

Human SECR in complex with an engineered Gs heterotrimer

Fukuhara, S., Kobayashi, K., Kusakizako, T., Shihoya, W., Nureki, O.

(2020) Biochem Biophys Res Commun 533: 861-866

Released	2020-11-04
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Bos taurus Homo sapiens Rattus norvegicus unidentified
Macromolecule	Unique protein chains: 6

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7D7P	Download File View File

Crystal structure of the phosphodiesterase domain of Salpingoeca rosetta rhodopsin phosphodiesterase

Ikuta, T., Shihoya, W., Yamashita, K., Nureki, O.

(2020) Nat Commun 11: 5605-5605

Released	2020-11-18
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Salpingoeca rosetta
Macromolecule	Phosphodiesterase (protein)
Unique Ligands	2PE, EDO, MG, PEG, ZN

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7D7Q	Download File View File

Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase

Ikuta, T., Shihoya, W., Yamashita, K., Nureki, O.

(2020) Nat Commun 11: 5605-5605

Released	2020-11-18
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Salpingoeca rosetta
Macromolecule	Phosphodiesterase (protein)
Unique Ligands	OLC, RET

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7DH5	Download File View File

Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer

Shihoya, W., Yamashita, K., Nureki, O.

(2021) Mol Cell 81: 3205-3215.e5

Released	2021-08-04
Method	ELECTRON MICROSCOPY 3.16 Å
Organisms	Bos taurus Canis lupus familiaris Homo sapiens Rattus norvegicus unidentified
Macromolecule	Beta-3 adrenergic receptor (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (protein) nanobody Nb35 (protein)
Unique Ligands	H6U

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7E4G	Download File View File

Crystal structure of schizorhodopsin 4

Shihoya, W., Nureki, O.

(2021) Proc Natl Acad Sci U S A 118:

Released	2021-02-24
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Promethearchaeati archaeon
Macromolecule	schizorhodopsin 4 (protein)
Unique Ligands	OLC, RET, SO4, ZN

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7E6X	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	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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