5H2O | pdb_00005h2o

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

PDB DOI: https://doi.org/10.2210/pdb5H2O/pdb

Classification: PROTON TRANSPORT
Organism(s): Halobacterium salinarum NRC-1
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2016-10-15 Released: 2016-12-21
Deposition Author(s): Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.184 (Depositor), 0.189 (DCC)
R-Value Work:
0.161 (Depositor), 0.166 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

A three-dimensional movie of structural changes in bacteriorhodopsin

Nango, E., Royant, A., Kubo, M., Nakane, T., Wickstrand, C., Kimura, T., Tanaka, T., Tono, K., Song, C., Tanaka, R., Arima, T., Yamashita, A., Kobayashi, J., Hosaka, T., Mizohata, E., Nogly, P., Sugahara, M., Nam, D., Nomura, T., Shimamura, T., Im, D., Fujiwara, T., Yamanaka, Y., Jeon, B., Nishizawa, T., Oda, K., Fukuda, M., Andersson, R., Bath, P., Dods, R., Davidsson, J., Matsuoka, S., Kawatake, S., Murata, M., Nureki, O., Owada, S., Kameshima, T., Hatsui, T., Joti, Y., Schertler, G., Yabashi, M., Bondar, A.N., Standfuss, J., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

PubMed: 28008064 Search on PubMed
DOI: https://doi.org/10.1126/science.aah3497
Primary Citation Related Structures:
5B6V, 5B6W, 5B6X, 5B6Y, 5B6Z, 5H2H, 5H2I, 5H2J, 5H2K, 5H2L, 5H2M, 5H2N, 5H2O, 5H2P

PubMed Abstract:
Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.

Organizational Affiliation

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.

Université Grenoble Alpes, CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, F-38044 Grenoble, France.

European Synchrotron Radiation Facility, F-38043 Grenoble, France.

Japan Science and Technology Agency (JST)-Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.

Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden.

Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.

Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.

Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea.

Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland.

Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden.

JST-Exploratory Research for Advanced Technology (ERATO), Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.

Department of Biology, ETH Zurich, 8093 Zürich, Switzerland.

Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany.

Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden. richard.neutze@gu.se s.iwata@spring8.or.jp.

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan. richard.neutze@gu.se s.iwata@spring8.or.jp.

Macromolecule Content

Total Structure Weight: 30.89 kDa
Atom Count: 2,562
Modeled Residue Count: 231
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	248	Halobacterium salinarum NRC-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore P02945 Go to UniProtKB: P02945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02945
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L2P Query on L2P Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain C [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain C [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	C [auth A], K [auth A], L [auth A]	2,3-DI-PHYTANYL-GLYCEROL C₄₃ H₈₈ O₃ ISDBCJSGCHUHFI-UMZPFTBHSA-N		Interactions Focus chain C [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth A] Focus chain K [auth A] Focus chain L [auth A]
RET Query on RET Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MYS Query on MYS Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A]	I [auth A], M [auth A]	PENTADECANE C₁₅ H₃₂ YCOZIPAWZNQLMR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth A] Interactions & Density Focus chain I [auth A] Focus chain M [auth A]
C14 Query on C14 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
TRD Query on TRD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TRIDECANE C₁₃ H₂₈ IIYFAKIEWZDVMP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
UND Query on UND Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain J [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain J [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain J [auth A]	J [auth A], Q [auth A]	UNDECANE C₁₁ H₂₄ RSJKGSCJYJTIGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain Q [auth A] Interactions & Density Focus chain J [auth A] Focus chain Q [auth A]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DD9 Query on DD9 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain P [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth A]	G [auth A], H [auth A], P [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth A]
HP6 Query on HP6 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]