RCSB PDB: Search

4X31 \| pdb_00004x31	Download File View File

Room temperature structure of bacteriorhodopsin from lipidic cubic phase obtained with serial millisecond crystallography using synchrotron radiation

Nogly, P., James, D., Wang, D., White, T., Zatsepin, N., Shilova, A., Nelson, G., Liu, H., Johansson, L., Heymann, M., Jaeger, K., Metz, M., Wickstrand, C., Wu, W., Baath, P., Berntsen, P., Oberthuer, D., Panneels, V., Cherezov, V., Chapman, H., Spence, J., Schertler, G., Neutze, R., Moraes, I., Burghammer, M., Standfuss, J., Weierstall, U.

(2015) IUCrJ 2: 168-176

Released	2015-02-18
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	LI1, RET

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4X32 \| pdb_00004x32	Download File View File

Bacteriorhodopsin ground state structure collected in cryo conditions from crystals obtained in LCP with PEG as a precipitant.

Nogly, P., Standfuss, J.

(2015) IUCrJ 2: 168-176

Released	2015-02-18
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	LI1, RET

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5B6V \| pdb_00005b6v	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: resting state structure

Nango, E., Royant, A., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5B6W \| pdb_00005b6w	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 16 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5B6X \| pdb_00005b6x	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 760 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5B6Y \| pdb_00005b6y	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 36.2 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5B6Z \| pdb_00005b6z	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 1.725 ms us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5H2H \| pdb_00005h2h	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 40 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5H2I \| pdb_00005h2i	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 110 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5H2J \| pdb_00005h2j	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 290 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5H2K \| pdb_00005h2k	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 2 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5H2L \| pdb_00005h2l	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 5.25 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5H2M \| pdb_00005h2m	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 13.8 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5H2N \| pdb_00005h2n	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 95.2 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5H2O \| pdb_00005h2o	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 250 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5H2P \| pdb_00005h2p	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 657 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

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5J7A \| pdb_00005j7a	Download File View File

Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography

Nogly, P., Panneels, V., Nelson, G., Gati, C., Kimura, T., Milne, C., Milathianaki, D., Kubo, M., Wu, W., Conrad, C., Coe, J., Bean, R., Zhao, Y., Bath, P., Dods, R., Harimoorthy, R., Beyerlein, K.R., Rheinberger, J., James, D., DePonte, D., Li, C., Sala, L., Williams, G., Hunter, M., Koglin, J.E., Berntsen, P., Nango, E., Iwata, S., Chapman, H.N., Fromme, P., Frank, M., Abela, R., Boutet, S., Barty, A., White, T.A., Weierstall, U., Spence, J., Neutze, R., Schertler, G., Standfuss, J.

(2016) Nat Commun 7: 12314-12314

Released	2016-08-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	LI1, RET

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5K5B \| pdb_00005k5b	Download File View File

Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP

Takala, H., Edlund, P., Claesson, E., Ihalainen, J.A., Westenhoff, S.

(2016) Sci Rep 6: 35279-35279

Released	2016-10-26
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Bacteriophytochrome (protein)
Unique Ligands	ACT, LBV, MPD

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5L8M \| pdb_00005l8m	Download File View File

Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at LCLS

Claesson, E., Takala, H., Edlund, P., Henry, L., Dods, R., Schmidt, M., Westenhoff, S.

(2016) Sci Rep 6: 35279-35279

Released	2016-10-26
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Deinococcus radiodurans
Macromolecule	Bacteriophytochrome (protein)
Unique Ligands	ACT, LBV

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5LBR \| pdb_00005lbr	Download File View File

Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at SACLA

Edlund, P., Claesson, E., Nakane, T., Takala, H., Dods, R., Schmidt, M., Westenhoff, S.

(2016) Sci Rep 6: 35279-35279

Released	2016-10-26
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Deinococcus radiodurans
Macromolecule	Bacteriophytochrome (protein)
Unique Ligands	ACT, LBV

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5NDC \| pdb_00005ndc	Download File View File

Structure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallography

Andersson, R., Safari, C., Dods, R., Nango, E., Tanaka, R., Nakane, T., Tono, K., Joti, Y., Bath, P., Dunevall, E., Bosman, E., Nureki, O., Iwata, S., Neutze, R., Branden, G.

(2017) Sci Rep 7: 4518-4518

Released	2017-08-23
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermus thermophilus
Macromolecule	Cytochrome c oxidase polypeptide IIA (protein) Cytochrome c oxidase subunit 1 (protein) Cytochrome c oxidase subunit 2 (protein)
Unique Ligands	CU, CUA, HAS, HEM, OLC

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5NJ4 \| pdb_00005nj4	Download File View File

From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography

Dods, R., Baath, P., Branden, G., Neutze, R.

(2017) Structure 25: 1461-1468.e2

Released	2017-08-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Blastochloris viridis
Macromolecule	Photosynthetic reaction center cytochrome c subunit (protein) Reaction center protein H chain (protein) Reaction center protein L chain (protein) Reaction center protein M chain (protein)
Unique Ligands	BCB, BPB, DGA, FE2, HEC, HTO, LDA, MQ7, NS5, SO4

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5O4C \| pdb_00005o4c	Download File View File

From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography

Dods, R., Baath, P., Branden, G., Neutze, R.

(2017) Structure 25: 1461-1468.e2

Released	2017-08-16
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Blastochloris viridis
Macromolecule	Photosynthetic reaction center cytochrome c subunit (protein) Reaction center protein H chain (protein) Reaction center protein L chain (protein) Reaction center protein M chain (protein)
Unique Ligands	BCB, BPB, DGA, FE2, HEC, HTO, LDA, MQ7, NS5, SO4

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5O64 \| pdb_00005o64	Download File View File

From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography

Dods, R., Baath, P., Branden, G., Neutze, R.

(2017) Structure 25: 1461-1468.e2

Released	2017-08-16
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Blastochloris viridis
Macromolecule	Photosynthetic reaction center cytochrome c subunit (protein) Reaction center protein H chain (protein) Reaction center protein L chain (protein) Reaction center protein M chain (protein)
Unique Ligands	BCB, BPB, DGA, FE2, FME, HEC, HTO, LDA, MQ7, NS5, SO4

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6G7H \| pdb_00006g7h	Download File View File

Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: resting state structure

Nogly, P., Weinert, T., James, D., Cabajo, S., Ozerov, D., Furrer, A., Gashi, D., Borin, V., Skopintsev, P., Jaeger, K., Nass, K., Bath, P., Bosman, R., Koglin, J., Seaberg, M., Lane, T., Kekilli, D., Bruenle, S., Tanaka, T., Wu, W., Milne, C., White, T., Barty, A., Weierstall, U., Panneels, V., Nango, E., Iwata, S., Hunter, M., Schapiro, I., Schertler, G., Neutze, R., Standfuss, J.

(2018) Science 361:

Released	2018-06-27
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	LI1, OLC, RET

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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

4X31 | pdb_00004x31

4X32 | pdb_00004x32

5B6V | pdb_00005b6v

5B6W | pdb_00005b6w

5B6X | pdb_00005b6x

5B6Y | pdb_00005b6y

5B6Z | pdb_00005b6z

5H2H | pdb_00005h2h

5H2I | pdb_00005h2i

5H2J | pdb_00005h2j

5H2K | pdb_00005h2k

5H2L | pdb_00005h2l

5H2M | pdb_00005h2m

5H2N | pdb_00005h2n

5H2O | pdb_00005h2o

5H2P | pdb_00005h2p

5J7A | pdb_00005j7a

5K5B | pdb_00005k5b

5L8M | pdb_00005l8m

5LBR | pdb_00005lbr

5NDC | pdb_00005ndc

5NJ4 | pdb_00005nj4

5O4C | pdb_00005o4c

5O64 | pdb_00005o64

6G7H | pdb_00006g7h