RCSB PDB: Search

4A4M \| pdb_00004a4m	Download File View File

Crystal structure of the light-activated constitutively active N2C, M257Y,D282C rhodopsin mutant in complex with a peptide resembling the C-terminus of the Galpha-protein subunit (GaCT)

Deupi, X., Edwards, P., Singhal, A., Nickle, B., Oprian, D.D., Schertler, G.F.X., Standfuss, J.

(2012) Proc Natl Acad Sci U S A 109: 119

Released	2012-01-25
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Bos taurus
Macromolecule	GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-3 (protein) RHODOPSIN (protein)
Unique Ligands	ACT, BOG, PLM, RET
Unique branched monosaccharides	NAG

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4BEY \| pdb_00004bey	Download File View File

Night blindness causing G90D rhodopsin in complex with GaCT2 peptide

Singhal, A., Ostermaier, M.K., Vishnivetskiy, S.A., Panneels, V., Homan, K.T., Tesmer, J.J.G., Veprintsev, D., Deupi, X., Gurevich, V.V., Schertler, G.F.X., Standfuss, J.

(2013) EMBO Rep 14: 520

Released	2013-05-08
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Bos taurus
Macromolecule	Guanine nucleotide-binding protein G(t) subunit alpha-1 (protein) Rhodopsin (protein)
Unique Ligands	ACT, BOG, PLM, SO4
Unique branched monosaccharides	BMA, MAN, NAG

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4BEZ \| pdb_00004bez	Download File View File

Night blindness causing G90D rhodopsin in the active conformation

Singhal, A., Ostermaier, M.K., Vishnivetskiy, S.A., Panneels, V., Homan, K.T., Tesmer, J.J.G., Veprintsev, D., Deupi, X., Gurevich, V.V., Schertler, G.F.X., Standfuss, J.

(2013) EMBO Rep 14: 520

Released	2013-04-24
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Bos taurus
Macromolecule	RHODOPSIN (protein)
Unique Ligands	ACT, BOG, PLM, SO4
Unique branched monosaccharides	BMA, MAN, NAG

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5DYS \| pdb_00005dys	Download File View File

Crystal Structure of T94I rhodopsin mutant

Singhal, A., Guo, Y., Matkovic, M., Schertler, G., Deupi, X., Yan, E., Standfuss, J.

(2016) EMBO Rep 17: 1431-1440

Released	2016-08-10
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bos taurus
Macromolecule	Rhodopsin (protein)
Unique Ligands	ACT, BOG, PLM, RET, SO4
Unique branched monosaccharides	BMA, MAN, NAG

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5EN0 \| pdb_00005en0	Download File View File

Crystal Structure of T94I rhodopsin mutant

Singhal, A., Guo, Y., Matkovic, M., Schertler, G., Deupi, X., Yan, E., Standfuss, J.

(2016) EMBO Rep 17: 1431-1440

Released	2016-08-10
Method	X-RAY DIFFRACTION 2.81 Å
Organisms	Bos taurus
Macromolecule	Guanine nucleotide-binding protein G(t) subunit alpha-3 (protein) Rhodopsin (protein)
Unique Ligands	ACT, BOG, PLM, RET, SO4
Unique branched monosaccharides	BMA, MAN, NAG

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6FUF \| pdb_00006fuf	Download File View File

Crystal structure of the rhodopsin-mini-Go complex

Tsai, C.-J., Weinert, T., Muehle, J., Pamula, F., Nehme, R., Flock, T., Nogly, P., Edwards, P.C., Carpenter, B., Gruhl, T., Ma, P., Deupi, X., Standfuss, J., Tate, C.G., Schertler, G.F.X.

(2018) Sci Adv 4: eaat7052-eaat7052

Released	2018-10-03
Method	X-RAY DIFFRACTION 3.117 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	Guanine nucleotide-binding protein G(o) subunit alpha (protein) Rhodopsin (protein)
Unique Ligands	NAG, RET

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6I9K \| pdb_00006i9k	Download File View File

Crystal structure of Jumping Spider Rhodopsin-1 bound to 9-cis retinal

Varma, N., Mutt, E., Muehle, J., Panneels, V., Terakita, A., Deupi, X., Nogly, P., Schertler, F.X.G., Lesca, E.

(2019) Proc Natl Acad Sci U S A 116: 14547-14556

Released	2019-07-03
Method	X-RAY DIFFRACTION 2.145 Å
Organisms	Hasarius adansoni
Macromolecule	Kumopsin1 (protein)
Unique Ligands	OLC, RET

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6QNK \| pdb_00006qnk	Download File View File

Antibody FAB fragment targeting Gi protein heterotrimer

Tsai, C.-J., Muehle, J., Pamula, F., Dawson, R.J.P., Maeda, S., Deupi, X., Schertler, G.F.X.

(2019) Elife 8:

Released	2019-07-10
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Mus musculus
Macromolecule	FAB heavy chain (protein) FAB light chain (protein)
Unique Ligands	EDO, MLT, PG4, PGE

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6QNO \| pdb_00006qno	Download File View File

Rhodopsin-Gi protein complex

Tsai, C.-J., Marino, J., Adaixo, R.J., Pamula, F., Muehle, J., Maeda, S., Flock, T., Taylor, N.M.I., Mohammed, I., Matile, H., Dawson, R.J.P., Deupi, X., Stahlberg, H., Schertler, G.F.X.

(2019) Elife 8:

Released	2019-07-10
Method	ELECTRON MICROSCOPY 4.38 Å
Organisms	Bos taurus Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 6
Unique Ligands	RET
Unique branched monosaccharides	NAG

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6TK1 \| pdb_00006tk1	Download File View File

Femtosecond to millisecond structural changes in a light-driven sodium pump: 20ms structure of KR2 with extrapolated, light and dark datasets

Skopintsev, P., Ehrenberg, D., Weinert, T., James, D., Kar, R., Johnson, P., Ozerov, D., Furrer, A., Martiel, I., Dworkowski, F., Nass, K., Knopp, G., Cirelli, C., Gashi, D., Mous, S., Wranik, M., Gruhl, T., Kekilli, D., Bruenle, S., Deupi, X., Schertler, G.F.X., Benoit, R., Panneels, V., Nogly, P., Schapiro, I., Milne, C., Heberle, J., Standfuss, J.

(2020) Nature 583: 314-318

Released	2020-05-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	LFA, NA, RET

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6TK2 \| pdb_00006tk2	Download File View File

Femtosecond to millisecond structural changes in a light-driven sodium pump: 1ms structure of KR2 with extrapolated, light and dark datasets

Skopintsev, P., Ehrenberg, D., Weinert, T., James, D., Kar, R., Johnson, P., Ozerov, D., Furrer, A., Martiel, I., Dworkowski, F., Nass, K., Knopp, G., Cirelli, C., Gashi, D., Mous, S., Wranik, M., Gruhl, T., Kekilli, D., Bruenle, S., Deupi, X., Schertler, G.F.X., Benoit, R., Panneels, V., Nogly, P., Schapiro, I., Milne, C., Heberle, J., Standfuss, J.

(2020) Nature 583: 314-318

Released	2020-05-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	LFA, NA, RET

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6TK3 \| pdb_00006tk3	Download File View File

Femtosecond to millisecond structural changes in a light-driven sodium pump: 30us+150us structure of KR2 with extrapolated, light and dark datasets

Skopintsev, P., Ehrenberg, D., Weinert, T., James, D., Kar, R., Johnson, P., Ozerov, D., Furrer, A., Martiel, I., Dworkowski, F., Nass, K., Knopp, G., Cirelli, C., Gashi, D., Mous, S., Wranik, M., Gruhl, T., Kekilli, D., Bruenle, S., Deupi, X., Schertler, G.F.X., Benoit, R., Panneels, V., Nogly, P., Schapiro, I., Milne, C., Heberle, J., Standfuss, J.

(2020) Nature 583: 314-318

Released	2020-05-27
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	LFA, RET

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6TK4 \| pdb_00006tk4	Download File View File

Femtosecond to millisecond structural changes in a light-driven sodium pump: 1ns+16ns structure of KR2 with extrapolated, light and dark datasets

Skopintsev, P., Ehrenberg, D., Weinert, T., James, D., Kar, R., Johnson, P., Ozerov, D., Furrer, A., Martiel, I., Dworkowski, F., Nass, K., Knopp, G., Cirelli, C., Gashi, D., Mous, S., Wranik, M., Gruhl, T., Kekilli, D., Bruenle, S., Deupi, X., Schertler, G.F.X., Benoit, R., Panneels, V., Nogly, P., Schapiro, I., Milne, C., Heberle, J., Standfuss, J.

(2020) Nature 583: 314-318

Released	2020-05-27
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	LFA, RET

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6TK5 \| pdb_00006tk5	Download File View File

Femtosecond to millisecond structural changes in a light-driven sodium pump: 800fs+2ps structure of KR2 with extrapolated, light and dark datasets

Skopintsev, P., Ehrenberg, D., Weinert, T., James, D., Kar, R., Johnson, P., Ozerov, D., Furrer, A., Martiel, I., Dworkowski, F., Nass, K., Knopp, G., Cirelli, C., Gashi, D., Mous, S., Wranik, M., Gruhl, T., Kekilli, D., Bruenle, S., Deupi, X., Schertler, G.F.X., Benoit, R., Panneels, V., Nogly, P., Schapiro, I., Milne, C., Heberle, J., Standfuss, J.

(2020) Nature 583: 314-318

Released	2020-05-27
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	LFA, RET

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6TK6 \| pdb_00006tk6	Download File View File

Femtosecond to millisecond structural changes in a light-driven sodium pump: Dark structure in neutral conditions with attached light datasets at 800fs, 2ps, 100ps, 1ns, 16ns, 1us, 30us, 150us, 1ms and 20ms

Skopintsev, P., Ehrenberg, D., Weinert, T., James, D., Kar, R., Johnson, P., Ozerov, D., Furrer, A., Martiel, I., Dworkowski, F., Nass, K., Knopp, G., Cirelli, C., Gashi, D., Mous, S., Wranik, M., Gruhl, T., Kekilli, D., Bruenle, S., Deupi, X., Schertler, G.F.X., Benoit, R., Panneels, V., Nogly, P., Schapiro, I., Milne, C., Heberle, J., Standfuss, J.

(2020) Nature 583: 314-318

Released	2020-05-27
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	LFA, RET

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6TK7 \| pdb_00006tk7	Download File View File

Femtosecond to millisecond structural changes in a light-driven sodium pump: Dark structure in acidic conditions

Skopintsev, P., Ehrenberg, D., Weinert, T., James, D., Kar, R., Johnson, P., Ozerov, D., Furrer, A., Martiel, I., Dworkowski, F., Nass, K., Knopp, G., Cirelli, C., Gashi, D., Mous, S., Wranik, M., Gruhl, T., Kekilli, D., Bruenle, S., Deupi, X., Schertler, G.F.X., Benoit, R., Panneels, V., Nogly, P., Schapiro, I., Milne, C., Heberle, J., Standfuss, J.

(2020) Nature 583: 314-318

Released	2020-05-27
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Dokdonia eikasta
Macromolecule	Sodium pumping rhodopsin (protein)
Unique Ligands	LFA, RET

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7O7F \| pdb_00007o7f	Download File View File

Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist

Isaikina, P., Tsai, C.-J., Dietz, N.B., Pamula, F., Goldie, K.N., Schertler, G.F.X., Maier, T., Stahlberg, H., Deupi, X., Grzesiek, S.

(2021) Sci Adv 7:

Released	2021-06-30
Method	ELECTRON MICROSCOPY 3.15 Å
Organisms	Bos taurus Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 7

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7ZBC \| pdb_00007zbc	Download File View File

Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA)

Gruhl, T., Weinert, T., Rodrigues, M.J., Milne, C., Ortolani, G., Nass, K., Nango, E., Sen, S., Johnson, P., Cirelli, C., Furrer, A., Mous, S., Skopintsev, P., James, D., Dworkowski, F., Baath, P., Kekilli, D., Oserov, D., Tanaka, R., Glover, H., Bacellar, C., Bruenle, S., Casadei, C., Diethelm, A., Gashi, D., Gotthard, G., Guixa-Gonzalez, R., Joti, Y., Kabanova, V., Knopp, G., Lesca, E., Ma, P., Martiel, I., Muehle, J., Owada, S., Pamula, F., Sarabi, S., Tejero, O., Tsai, C.J., Varma, N., Wach, A., Boutet, S., Tono, K., Nogly, P., Deupi, X., Iwata, S., Neutze, R., Standfuss, J., Schertler, G.F.X., Panneels, V.

(2023) Nature 615: 939-944

Released	2023-03-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	Rhodopsin (protein)
Unique Ligands	ACE, DAO, NAG, OLC, PLM, RET
Unique branched monosaccharides	NAG

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7ZBE \| pdb_00007zbe	Download File View File

Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SwissFEL)

Gruhl, T., Weinert, T., Rodrigues, M.J., Milne, C., Ortolani, G., Nass, K., Nango, E., Sen, S., Johnson, P., Cirelli, C., Furrer, A., Mous, S., Skopintsev, P., James, D., Dworkowski, F., Baath, P., Kekilli, D., Oserov, D., Tanaka, R., Glover, H., Bacellar, C., Bruenle, S., Casadei, C., Diethelm, A., Gashi, D., Gotthard, G., Guixa-Gonzalez, R., Joti, Y., Kabanova, V., Knopp, G., Lesca, E., Ma, P., Martiel, I., Muehle, J., Owada, S., Pamula, F., Sarabi, D., Tejero, O., Tsai, C.J., Varma, N., Wach, A., Boutet, S., Tono, K., Nogly, P., Deupi, X., Iwata, S., Neutze, R., Standfuss, J., Schertler, G.F.X., Panneels, V.

(2023) Nature 615: 939-944

Released	2023-03-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	Rhodopsin (protein)
Unique Ligands	ACE, DAO, NAG, OLC, PLM, RET
Unique branched monosaccharides	NAG

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8A6C \| pdb_00008a6c	Download File View File

1 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase

Gruhl, T., Weinert, T., Rodrigues, M.J., Milne, C.J., Ortolani, G., Nass, K., Nango, E., Sen, S., Johnson, P.J.M., Cirelli, C., Furrer, A., Mous, S., Skopintsev, P., James, D., Dworkowski, F., Baath, P., Kekilli, D., Oserov, D., Tanaka, R., Glover, H., Bacellar, C., Bruenle, S., Casadei, C.M., Diethelm, A.D., Gashi, D., Gotthard, G., Guixa-Gonzalez, R., Joti, Y., Kabanova, V., Knopp, G., Lesca, E., Ma, P., Martiel, I., Muehle, J., Owada, S., Pamula, F., Sarabi, D., Tejero, O., Tsai, C.J., Varma, N., Wach, A., Boutet, S., Tono, K., Nogly, P., Deupi, X., Iwata, S., Neutze, R., Standfuss, J., Schertler, G.F.X., Panneels, V.

(2023) Nature 615: 939-944

Released	2023-03-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	Rhodopsin (protein)
Unique Ligands	ACE, DAO, NAG, OLC, PLM, RET
Unique branched monosaccharides	NAG

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8A6D \| pdb_00008a6d	Download File View File

10 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase

Gruhl, T., Weinert, T., Rodrigues, M.J., Milne, C.J., Ortolani, G., Nass, K., Nango, E., Sen, S., Johnson, P.J.M., Cirelli, C., Furrer, A., Mous, S., Skopintsev, P., James, D., Dworkowski, F., Baath, P., Kekilli, D., Oserov, D., Tanaka, R., Glover, H., Bacellar, C., Bruenle, S., Casadei, C.M., Diethelm, A.D., Gashi, D., Gotthard, G., Guixa-Gonzalez, R., Joti, Y., Kabanova, V., Knopp, G., Lesca, E., Ma, P., Martiel, I., Muehle, J., Owada, S., Pamula, F., Sarabi, D., Tejero, O., Tsai, C.J., Varma, N., Wach, A., Boutet, S., Tono, K., Nogly, P., Deupi, X., Iwata, S., Neutze, R., Standfuss, J., Schertler, G.F.X., Panneels, V.

(2023) Nature 615: 939-944

Released	2023-03-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	Rhodopsin (protein)
Unique Ligands	ACE, DAO, NAG, OLC, PLM, RET
Unique branched monosaccharides	NAG

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8A6E \| pdb_00008a6e	Download File View File

100 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA)

Gruhl, T., Weinert, T., Rodrigues, M.J., Milne, C.J., Ortolani, G., Nass, K., Nango, E., Sen, S., Johnson, P.J.M., Cirelli, C., Furrer, A., Mous, S., Skopintsev, P., James, D., Dworkowski, F., Baath, P., Kekilli, D., Oserov, D., Tanaka, R., Glover, H., Bacellar, C., Bruenle, S., Casadei, C.M., Diethelm, A.D., Gashi, D., Gotthard, G., Guixa-Gonzalez, R., Joti, Y., Kabanova, V., Knopp, G., Lesca, E., Ma, P., Martiel, I., Muehle, J., Owada, S., Pamula, F., Sarabi, D., Tejero, O., Tsai, C.J., Varma, N., Wach, A., Boutet, S., Tono, K., Nogly, P., Deupi, X., Iwata, S., Neutze, R., Standfuss, J., Schertler, G.F.X., Panneels, V.

(2023) Nature 615: 939-944

Released	2023-03-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	Rhodopsin (protein)
Unique Ligands	DAO, NAG, OLC, PLM, RET
Unique branched monosaccharides	NAG

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8QEG \| pdb_00008qeg	Download File View File

Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor

Muehle, J., Rodrigues, M.J., Guixa-Gonzalez, R., Deupi, X., Schertler, G.F.X.

To be published

Released	2025-03-19
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	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 subunit alpha-11 (protein)
Unique Ligands	ACE, ALA, DAM, EDO, GDP, HF2, HL2, MAA, OTH, THC

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8QEH \| pdb_00008qeh	Download File View File

Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor

Muehle, J., Rodrigues, M.J., Guixa-Gonzalez, R., Deupi, X., Schertler, G.F.X.

To be published

Released	2025-03-19
Method	X-RAY DIFFRACTION 1.43 Å
Organisms	Homo sapiens
Macromolecule	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 subunit alpha-11 (protein)
Unique Ligands	ALA, CL, DAM, DMS, EDO, GDP, HF2, HL2, MAA, OTH, PPI, UDL, ZN

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9EPP \| pdb_00009epp	Download File View File

Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Giq heterotrimer

Tejero, O., Pamula, F., Koyanagi, M., Nagata, T., Afanasyev, P., Das, I., Deupi, X., Sheves, M., Terakita, A., Schertler, G.F.X., Rodrigues, M.J., Tsai, C.-J.

(2024) Nat Commun 15: 8928-8928

Released	2024-10-23
Method	ELECTRON MICROSCOPY 4.06 Å
Organisms	Hasarius adansoni Homo sapiens
Macromolecule	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(i) subunit alpha-1 (protein) Kumopsin1 (protein)
Unique Ligands	A1H6M

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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

4A4M | pdb_00004a4m

4BEY | pdb_00004bey

4BEZ | pdb_00004bez

5DYS | pdb_00005dys

5EN0 | pdb_00005en0

6FUF | pdb_00006fuf

6I9K | pdb_00006i9k

6QNK | pdb_00006qnk

6QNO | pdb_00006qno

6TK1 | pdb_00006tk1

6TK2 | pdb_00006tk2

6TK3 | pdb_00006tk3

6TK4 | pdb_00006tk4

6TK5 | pdb_00006tk5

6TK6 | pdb_00006tk6

6TK7 | pdb_00006tk7

7O7F | pdb_00007o7f

7ZBC | pdb_00007zbc

7ZBE | pdb_00007zbe

8A6C | pdb_00008a6c

8A6D | pdb_00008a6d

8A6E | pdb_00008a6e

8QEG | pdb_00008qeg

8QEH | pdb_00008qeh

9EPP | pdb_00009epp