5ZTK

Synchrotron structure of light-driven chloride pump having an NTQ motif

Summary for 5ZTK

• Entry DOI: 10.2210/pdb5ztk/pdb
• Descriptor: Chloride pumping rhodopsin, CHLORIDE ION, RETINAL, ... (5 entities in total)
• Functional Keywords: chloride pump, signaling protein
• Biological source: Nonlabens marinus S1-08
• Total number of polymer chains: 1
• Total formula weight: 32822.33

Authors

Yun, J.H.,Park, J.H.,Park, S.Y.,Lee, W. (deposition date: 2018-05-04, release date: 2018-12-05, Last modification date: 2024-10-30)

Primary citation

Yun, J.H.,Li, X.,Park, J.H.,Wang, Y.,Ohki, M.,Jin, Z.,Lee, W.,Park, S.Y.,Hu, H.,Li, C.,Zatsepin, N.,Hunter, M.S.,Sierra, R.G.,Koralek, J.,Yoon, C.H.,Cho, H.S.,Weierstall, U.,Tang, L.,Liu, H.,Lee, W.
Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency
J. Biol. Chem., 294:794-804, 2019

PubMed Abstract: Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all- retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.

PubMed: 30455349
DOI: 10.1074/jbc.RA118.004038

Experimental method

X-RAY DIFFRACTION (1.75 Å)