RCSB PDB: Search

3QAP \| pdb_00003qap	Download File View File

Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the ground state

Gushchin, I., Reshetnyak, A., Borshchevskiy, V., Ishchenko, A., Round, E., Grudinin, S., Engelhard, M., Buldt, G., Gordeliy, V.

(2011) J Mol Biology 412: 591-600

Released	2011-09-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin-2 (protein)
Unique Ligands	BOG, L2P, LFA, RET

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3QDC \| pdb_00003qdc	Download File View File

Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the active state

Gushchin, I., Reshetnyak, A., Borshchevskiy, V., Ishchenko, A., Round, E., Grudinin, S., Engelhard, M., Buldt, G., Gordeliy, V.

(2011) J Mol Biology 412: 591-600

Released	2011-09-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin-2 (protein)
Unique Ligands	BOG, L2P, LFA, RET

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4GYC \| pdb_00004gyc	Download File View File

Structure of the SRII(D75N mutant)/HtrII Complex in I212121 space group ("U" shape)

Ishchenko, A., Round, E., Borshchevskiy, V., Grudinin, S., Gushchin, I., Klare, J., Remeeva, A., Utrobin, P., Balandin, T., Engelhard, M., Bueldt, G., Gordeliy, V.

(2013) J Photochem Photobiol B 123C: 55-58

Released	2013-05-08
Method	X-RAY DIFFRACTION 2.0501 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin II transducer (protein) Sensory rhodopsin-2 (protein)
Unique Ligands	LFA, RET

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4MD1 \| pdb_00004md1	Download File View File

Orange species of bacteriorhodopsin from Halobacterium salinarum

Borshchevskiy, V., Erofeev, I., Round, E., Weik, M., Ishchenko, A., Gushchin, I., Mishin, A., Bueldt, G., Gordeliy, V.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2675-2685

Released	2014-10-08
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	L2P, RET, SQL

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4MD2 \| pdb_00004md2	Download File View File

Ground state of bacteriorhodopsin from Halobacterium salinarum

Borshchevskiy, V., Erofeev, I., Round, E., Weik, M., Ishchenko, A., Gushchin, I., Mishin, A., Bueldt, G., Gordeliy, V.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2675-2685

Released	2014-10-08
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	L2P, RET, SQL

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4MND \| pdb_00004mnd	Download File View File

Crystal structure of Archaeoglobus fulgidus IPCT-DIPPS bifunctional membrane protein

Nogly, P., Gushchin, I., Remeeva, A., Esteves, A.M., Ishchenko, A., Ma, P., Grudinin, S., Borges, N., Round, E., Moraes, I., Borshchevskiy, V., Santos, H., Gordeliy, V., Archer, M.

(2014) Nat Commun 5: 4169-4169

Released	2014-07-02
Method	X-RAY DIFFRACTION 2.66 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CTP L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase (protein)
Unique Ligands	LFA, MG

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4RWA \| pdb_00004rwa	Download File View File

Synchrotron structure of the human delta opioid receptor in complex with a bifunctional peptide (PSI community target)

Fenalti, G., Zatsepin, N.A., Betti, C., Giguere, P., Han, G.W., Ishchenko, A., Liu, W., Guillemyn, K., Zhang, H., James, D., Wang, D., Weierstall, U., Spence, J.C.H., Boutet, S., Messerschmidt, M., Williams, G.J., Gati, C., Yefanov, O.M., White, T.A., Oberthuer, D., Metz, M., Yoon, C.H., Barty, A., Chapman, H.N., Basu, S., Coe, J., Conrad, C.E., Fromme, R., Fromme, P., Tourwe, D., Schiller, P.W., Roth, B.L., Ballet, S., Katritch, V., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

(2015) Nat Struct Mol Biol 22: 265-268

Released	2015-01-14
Method	X-RAY DIFFRACTION 3.28 Å
Organisms	Escherichia coli Homo sapiens synthetic construct
Macromolecule	Soluble cytochrome b562,Delta-type opioid receptor (protein) bifunctional peptide (protein)
Unique Ligands	OLC

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4RWD \| pdb_00004rwd	Download File View File

XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide

Fenalti, G., Zatsepin, N.A., Betti, C., Giguere, P., Han, G.W., Ishchenko, A., Liu, W., Guillemyn, K., Zhang, H., James, D., Wang, D., Weierstall, U., Spence, J.C.H., Boutet, S., Messerschmidt, M., Williams, G.J., Gati, C., Yefanov, O.M., White, T.A., Oberthuer, D., Metz, M., Yoon, C.H., Barty, A., Chapman, H.N., Basu, S., Coe, J., Conrad, C.E., Fromme, R., Fromme, P., Tourwe, D., Schiller, P.W., Roth, B.L., Ballet, S., Katritch, V., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

(2015) Nat Struct Mol Biol 22: 265-268

Released	2015-01-14
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli Homo sapiens synthetic construct
Macromolecule	Soluble cytochrome b562,Delta-type opioid receptor (protein) bifunctional peptide (protein)
Unique Ligands	NA, OLA, OLC

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4YAY \| pdb_00004yay	Download File View File

XFEL structure of human Angiotensin Receptor

Zhang, H., Unal, H., Gati, C., Han, G.W., Zatsepin, N.A., James, D., Wang, D., Nelson, G., Weierstall, U., Messerschmidt, M., Williams, G.J., Boutet, S., Yefanov, O.M., White, T.A., Liu, W., Ishchenko, A., Tirupula, K.C., Desnoyer, R., Sawaya, M.C., Xu, Q., Coe, J., Cornrad, C.E., Fromme, P., Stevens, R.C., Katritch, V., Karnik, S.S., Cherezov, V., GPCR Network (GPCR)

(2015) Cell 161: 833-844

Released	2015-04-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Soluble cytochrome b562,Type-1 angiotensin II receptor (protein)
Unique Ligands	ZD7

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4ZIX \| pdb_00004zix	Download File View File

Structure of HEWL using Serial Femtosecond Crystallography of Soluble Proteins in Lipidic Cubic Phase

Fromme, R., Ishchenko, A., Metz, M., Roy-Chowdhury, S., Basu, S., Boutet, S., Fromme, P., White, T.A., Barty, A., Spence, J.C.H., Weierstall, U., Liu, W., Cherezov, V.

(2015) IUCrJ 2: 545

Released	2015-08-12
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)
Unique Ligands	CL, NA

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4ZIZ \| pdb_00004ziz	Download File View File

Serial Femtosecond Crystallography of Soluble Proteins in Lipidic Cubic Phase (C-Phycocyanin from T. elongatus)

Fromme, R., Ishchenko, A., Metz, M., Roy-Chowdhury, S., Basu, S., Boutet, S., Fromme, P., White, T.A., Barty, A., Spence, J.C.H., Weierstall, U., Liu, W., Cherezov, V.

(2015) IUCrJ 2: 545-551

Released	2015-08-19
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	C-phycocyanin alpha chain (protein) C-phycocyanin beta chain (protein)
Unique Ligands	CYC

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4ZWJ \| pdb_00004zwj	Download File View File

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

Kang, Y., Zhou, X.E., Gao, X., He, Y., Liu, W., Ishchenko, A., Barty, A., White, T.A., Yefanov, O., Han, G.W., Xu, Q., de Waal, P.W., Ke, J., Tan, M.H.E., Zhang, C., Moeller, A., West, G.M., Pascal, B., Eps, N.V., Caro, L.N., Vishnivetskiy, S.A., Lee, R.J., Suino-Powell, K.M., Gu, X., Pal, K., Ma, J., Zhi, X., Boutet, S., Williams, G.J., Messerschmidt, M., Gati, C., Zatsepin, N.A., Wang, D., James, D., Basu, S., Roy-Chowdhury, S., Conrad, C., Coe, J., Liu, H., Lisova, S., Kupitz, C., Grotjohann, I., Fromme, R., Jiang, Y., Tan, M., Yang, H., Li, J., Wang, M., Zheng, Z., Li, D., Howe, N., Zhao, Y., Standfuss, J., Diederichs, K., Dong, Y., Potter, C.S., Carragher, B., Caffrey, M., Jiang, H., Chapman, H.N., Spence, J.C.H., Fromme, P., Weierstall, U., Ernst, O.P., Katritch, V., Gurevich, V.V., Griffin, P.R., Hubbell, W.L., Stevens, R.C., Cherezov, V., Melcher, K., Xu, H.E., GPCR Network (GPCR)

(2015) Nature 523: 561-567

Released	2015-07-29
Method	X-RAY DIFFRACTION 3.302 Å
Organisms	Homo sapiens Mus musculus Tequatrovirus T4
Macromolecule	Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin (protein)

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5IJI \| pdb_00005iji	Download File View File

Fragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in symmetric holo state

Gushchin, I., Melnikov, I., Polovinkin, V., Ishchenko, A., Popov, A., Gordeliy, V.

(2017) Science 356:

Released	2017-05-31
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Escherichia coli
Macromolecule	Nitrate/nitrite sensor histidine kinase NarQ (protein)
Unique Ligands	LFA, NO3

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5JEF \| pdb_00005jef	Download File View File

Fragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in asymmetric holo state

Gushchin, I., Melnikov, I., Polovinkin, V., Ishchenko, A., Popov, A., Gordeliy, V.

(2017) Science 356:

Released	2017-05-31
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Escherichia coli K-12
Macromolecule	Nitrate/nitrite sensor protein NarQ (protein)
Unique Ligands	LFA, NO3

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5JEQ \| pdb_00005jeq	Download File View File

Fragment of nitrate/nitrite sensor histidine kinase NarQ (R50K) in symmetric apo state

Gushchin, I., Melnikov, I., Polovinkin, V., Ishchenko, A., Popov, A., Gordeliy, V.

(2017) Science 356:

Released	2017-05-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	Nitrate/nitrite sensor protein NarQ (protein)
Unique Ligands	PO4

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5JJE \| pdb_00005jje	Download File View File

Structure of the SRII/HtrII Complex in I212121 space group ("U" shape)

Ishchenko, A., Round, E., Borshchevskiy, V., Grudinin, S., Gushchin, I., Klare, J., Remeeva, A., Polovinkin, V., Utrobin, P., Balandin, T., Engelhard, M., Bueldt, G., Gordeliy, V.

(2017) Sci Rep 7: 41811-41811

Released	2017-02-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin II transducer (protein) Sensory rhodopsin-2 (protein)
Unique Ligands	BOG, LFA, RET

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5JJF \| pdb_00005jjf	Download File View File

Structure of the SRII/HtrII Complex in I212121 space group ("U" shape) - M state

Ishchenko, A., Round, E., Borshchevskiy, V., Grudinin, S., Gushchin, I., Klare, J., Remeeva, A., Polovinkin, V., Utrobin, P., Balandin, T., Engelhard, M., Bueldt, G., Gordeliy, V.

(2017) Sci Rep 7: 41811-41811

Released	2017-02-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin II transducer (protein) Sensory rhodopsin-2 (protein)
Unique Ligands	BOG, LFA, RET

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5JJJ \| pdb_00005jjj	Download File View File

Structure of the SRII/HtrII Complex in P64 space group ("U" shape)

Ishchenko, A., Round, E., Borshchevskiy, V., Grudinin, S., Gushchin, I., Klare, J., Remeeva, A., Polovinkin, V., Utrobin, P., Balandin, T., Engelhard, M., Bueldt, G., Gordeliy, V.

(2017) Sci Rep 7: 41811-41811

Released	2017-02-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin II transducer (protein) Sensory rhodopsin-2 (protein)
Unique Ligands	LFA, RET

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5JJN \| pdb_00005jjn	Download File View File

Structure of the SRII/HtrII(G83F) Complex in P212121 space group ("V" shape)

Ishchenko, A., Round, E., Borshchevskiy, V., Grudinin, S., Gushchin, I., Klare, J., Remeeva, A., Polovinkin, V., Utrobin, P., Balandin, T., Engelhard, M., Bueldt, G., Gordeliy, V.

(2017) Sci Rep 7: 41811-41811

Released	2017-02-15
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Natronomonas pharaonis
Macromolecule	Sensory rhodopsin II transducer (protein) Sensory rhodopsin-2 (protein)
Unique Ligands	BOG, LFA, RET

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5K2A \| pdb_00005k2a	Download File View File

2.5 angstrom A2a adenosine receptor structure with sulfur SAD phasing using XFEL data

Batyuk, A., Galli, L., Ishchenko, A., Han, G.W., Gati, C., Popov, P., Lee, M.-Y., Stauch, B., White, T.A., Barty, A., Aquila, A., Hunter, M.S., Liang, M., Boutet, S., Pu, M., Liu, Z.-J., Nelson, G., James, D., Li, C., Zhao, Y., Spence, J.C.H., Liu, W., Fromme, P., Katritch, V., Weierstall, U., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

(2016) Sci Adv 2: e1600292-e1600292

Released	2016-09-21
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Adenosine receptor A2a/Soluble cytochrome b562 chimera (protein)
Unique Ligands	CLR, NA, OLA, OLC, PEG, ZMA

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5K2B \| pdb_00005k2b	Download File View File

2.5 angstrom A2a adenosine receptor structure with MR phasing using XFEL data

Batyuk, A., Galli, L., Ishchenko, A., Han, G.W., Gati, C., Popov, P., Lee, M.-Y., Stauch, B., White, T.A., Barty, A., Aquila, A., Hunter, M.S., Liang, M., Boutet, S., Pu, M., Liu, Z.-J., Nelson, G., James, D., Li, C., Zhao, Y., Spence, J.C.H., Liu, W., Fromme, P., Katritch, V., Weierstall, U., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

(2016) Sci Adv 2: e1600292-e1600292

Released	2016-09-21
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Adenosine receptor A2a/Soluble cytochrome b562 chimera (protein)
Unique Ligands	CLR, NA, OLA, OLB, OLC, ZMA

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5K2C \| pdb_00005k2c	Download File View File

1.9 angstrom A2a adenosine receptor structure with sulfur SAD phasing and phase extension using XFEL data

Batyuk, A., Galli, L., Ishchenko, A., Han, G.W., Gati, C., Popov, P., Lee, M.-Y., Stauch, B., White, T.A., Barty, A., Aquila, A., Hunter, M.S., Liang, M., Boutet, S., Pu, M., Liu, Z.-J., Nelson, G., James, D., Li, C., Zhao, Y., Spence, J.C.H., Liu, W., Fromme, P., Katritch, V., Weierstall, U., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

(2016) Sci Adv 2: e1600292-e1600292

Released	2016-09-21
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Adenosine receptor A2a/Soluble cytochrome b562 chimera (protein)
Unique Ligands	CLR, NA, OLA, OLC, PEG, ZMA

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5K2D \| pdb_00005k2d	Download File View File

1.9A angstrom A2a adenosine receptor structure with MR phasing using XFEL data

Batyuk, A., Galli, L., Ishchenko, A., Han, G.W., Gati, C., Popov, P., Lee, M.-Y., Stauch, B., White, T.A., Barty, A., Aquila, A., Hunter, M.S., Liang, M., Boutet, S., Pu, M., Liu, Z.-J., Nelson, G., James, D., Li, C., Zhao, Y., Spence, J.C.H., Liu, W., Fromme, P., Katritch, V., Weierstall, U., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

(2016) Sci Adv 2: e1600292-e1600292

Released	2016-09-21
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Adenosine receptor A2a/Soluble cytochrome b562 chimera (protein)
Unique Ligands	CLR, NA, OLA, OLB, OLC, PEG, ZMA

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5TUD \| pdb_00005tud	Download File View File

Structural Insights into the Extracellular Recognition of the Human Serotonin 2B Receptor by an Antibody

Ishchenko, A., Wacker, D., Kapoor, M., Zhang, A., Han, G.W., Basu, S., Boutet, S., James, D., Wang, D., Weierstall, U., Liu, W., Katritch, V., Stevens, R.C., Cherezov, V.

(2017) Proc Natl Acad Sci U S A 114: 8223-8228

Released	2017-07-26
Method	X-RAY DIFFRACTION 3 Å
Organisms	Escherichia coli Homo sapiens Mus musculus
Macromolecule	5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera (protein) Anti-5-HT2B Fab heavy chain (protein) Anti-5-HT2B Fab light chain (protein)
Unique Ligands	ERM

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5UNF \| pdb_00005unf	Download File View File

XFEL structure of human angiotensin II type 2 receptor (Monoclinic form) in complex with compound 1 (N-benzyl-N-(2-ethyl-4-oxo-3-{[2'-(2H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl])

Zhang, H., Han, G.W., Batyuk, A., Ishchenko, A., White, K.L., Patel, N., Sadybekov, A., Zamlynny, B., Rudd, M.T., Hollenstein, K., Tolstikova, A., White, T.A., Hunter, M.S., Weierstall, U., Liu, W., Babaoglu, K., Moore, E.L., Katz, R.D., Shipman, J.M., Garcia-Calvo, M., Sharma, S., Sheth, P., Soisson, S.M., Stevens, R.C., Katritch, V., Cherezov, V.

(2017) Nature 544: 327-332

Released	2017-04-05
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Chimera protein of Type-2 angiotensin II receptor and Soluble cytochrome b562 (protein)
Unique Ligands	8ES

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Structure Determination Methodology

Scientific Name of Source Organism

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Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

3QAP | pdb_00003qap

3QDC | pdb_00003qdc

4GYC | pdb_00004gyc

4MD1 | pdb_00004md1

4MD2 | pdb_00004md2

4MND | pdb_00004mnd

4RWA | pdb_00004rwa

4RWD | pdb_00004rwd

4YAY | pdb_00004yay

4ZIX | pdb_00004zix

4ZIZ | pdb_00004ziz

4ZWJ | pdb_00004zwj

5IJI | pdb_00005iji

5JEF | pdb_00005jef

5JEQ | pdb_00005jeq

5JJE | pdb_00005jje

5JJF | pdb_00005jjf

5JJJ | pdb_00005jjj

5JJN | pdb_00005jjn

5K2A | pdb_00005k2a

5K2B | pdb_00005k2b

5K2C | pdb_00005k2c

5K2D | pdb_00005k2d

5TUD | pdb_00005tud

5UNF | pdb_00005unf