9I6H

Room temperature structure of KR2 rhodopsin in pentameric form at 95% relative humidity

Summary for 9I6H

• Entry DOI: 10.2210/pdb9i6h/pdb
• Descriptor: Sodium pumping rhodopsin, RETINAL, SODIUM ION, ... (6 entities in total)
• Functional Keywords: sodium pump, membrane protein
• Biological source: Dokdonia eikasta
• Total number of polymer chains: 5
• Total formula weight: 179874.06

Authors

Zabelskii, D.,Round, E.,Han, H.,von Stetten, D.,Melo, D.,de Wijn, R.,Bean, R.,Round, A. (deposition date: 2025-01-30, release date: 2025-07-16, Last modification date: 2025-11-26)

Primary citation

Zabelskii, D.,Round, E.,Han, H.,von Stetten, D.,Letrun, R.,Kim, C.,Sato, T.,V M Melo, D.,de Wijn, R.,Kharitonov, K.,Smyth, P.,Doerner, K.,Kloos, M.,Dietze, T.,Morillo, L.L.,Bean, R.,Round, A.
Viscoelastic characterization of the lipid cubic phase provides insights into high-viscosity extrusion injection for XFEL experiments.
Sci Rep, 15:38999-38999, 2025

PubMed Abstract: Serial crystallography (SX) is a powerful method for determining macromolecular structures, enabled by the advent of X-ray free-electron lasers (XFELs). SX experiments require the continuous delivery of microcrystals, achievable through liquid jets, high-viscosity extrusion (HVE) jets, and fixed-target methods. The lipid cubic phase (LCP) is a lipid-based medium commonly used for membrane protein crystallization and as a carrier medium for HVE injection. In this study, we present a rheometric characterization of LCP media and demonstrate that sample viscosity correlates well with the injection stability and, therefore, can effectively predict sample stability during HVE jetting. Using this approach, we determined the viscosity range corresponding to the stable, metastable, and unstable jetting regions. The critical viscosity values for the metastable and unstable jetting regions are 7 × 10 and 10 mPa⋅s, measured at the 0.3 s shear rate. We show that ambient humidity is crucial for rheometric and fixed-target experiments involving LCP-embedded crystals. Specifically, LCP-embedded crystals rapidly lose diffraction quality when exposed to ambient humidity below 80%. Additionally, we demonstrate that sample viscosity measured in the rheometric experiment can help determine the necessary amount of stabilizing additive for HVE jet optimization. This approach was successfully tested on LCP mixed with long-chain polyethylene glycol and stabilized with Pluronic F-127 polymer.

PubMed: 41203717
DOI: 10.1038/s41598-025-25449-8

Experimental method

X-RAY DIFFRACTION (3 Å)