7VGV

Anion free form of light-driven chloride ion-pumping rhodopsin, NM-R3, structure determined by serial femtosecond crystallography at SACLA

Summary for 7VGV

• Entry DOI: 10.2210/pdb7vgv/pdb
• Descriptor: Chloride pumping rhodopsin, RETINAL, HEXANE, ... (9 entities in total)
• Functional Keywords: sacla serial femtosecond crystallography cell-free synthesis bacterial type rhodopsin chloride ion pump rhodopsin, membrane protein
• Biological source: Nonlabens marinus S1-08
• Total number of polymer chains: 3
• Total formula weight: 94696.28

Authors

Hosaka, T.,Nango, E.,Nakane, T.,Luo, F.,Kimura-Someya, T.,Shirouzu, M. (deposition date: 2021-09-18, release date: 2022-02-16, Last modification date: 2024-10-23)

Primary citation

Hosaka, T.,Nomura, T.,Kubo, M.,Nakane, T.,Fangjia, L.,Sekine, S.I.,Ito, T.,Murayama, K.,Ihara, K.,Ehara, H.,Kashiwagi, K.,Katsura, K.,Akasaka, R.,Hisano, T.,Tanaka, T.,Tanaka, R.,Arima, T.,Yamashita, A.,Sugahara, M.,Naitow, H.,Matsuura, Y.,Yoshizawa, S.,Tono, K.,Owada, S.,Nureki, O.,Kimura-Someya, T.,Iwata, S.,Nango, E.,Shirouzu, M.
Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers.
Proc.Natl.Acad.Sci.USA, 119:-, 2022

PubMed Abstract: Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10-µs and 1-ms time points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied by a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3.

PubMed: 35197289
DOI: 10.1073/pnas.2117433119

Experimental method

X-RAY DIFFRACTION (2.3 Å)