9I6H | pdb_00009i6h

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

• PDB DOI: https://doi.org/10.2210/pdb9I6H/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Dokdonia eikasta
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-30 Released: 2025-07-16 
• Deposition Author(s): Zabelskii, D., Round, E., Han, H., von Stetten, D., Melo, D., de Wijn, R., Bean, R., Round, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Viscoelastic characterization of the lipid cubic phase provides insights into high-viscosity extrusion injection for XFEL experiments.

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.

(2025) Sci Rep 15: 38999-38999

• PubMed: 41203717 
• DOI: https://doi.org/10.1038/s41598-025-25449-8
• Primary Citation Related Structures: 
  9I6H, 9I6I, 9I6J, 9I6K, 9I6L, 9I6M, 9I6N, 9I6O, 9I6P


• 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 ⁵ and 10 ⁴  mPa⋅s, measured at the 0.3 s ^-1 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.

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Organizational Affiliation: 
• European XFEL GmbH, Schenefeld, Germany. [e-mail].
European XFEL GmbH, Schenefeld, Germany.
European Molecular Biology Laboratory, Hamburg Unit C/O DESY, Hamburg, Germany.
European XFEL GmbH, Schenefeld, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 179.87 kDa 
• Atom Count: 11,939 
• Modeled Residue Count: 1,342 
• Deposited Residue Count: 1,365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium pumping rhodopsin	A, B, C, D, E	273	Dokdonia eikasta	Mutation(s): 0  Gene Names: NaR
UniProt
Find proteins for N0DKS8 (Dokdonia eikasta) Explore N0DKS8  Go to UniProtKB:  N0DKS8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	AB [auth C], AC [auth E], BC [auth E], CA [auth B], CC [auth E], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], H [auth A], HB [auth D], I [auth A], IB [auth D], J [auth A], JB [auth D], K [auth A], KA [auth B], KB [auth D], KC [auth E], L [auth A], LA [auth B], LB [auth D], LC [auth E], M [auth A], MB [auth D], N [auth A], O [auth A], OA [auth B], P [auth A], Q [auth A], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WB [auth E], X [auth A], XB [auth E], YB [auth E], Z [auth A], ZB [auth E]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET (Subject of Investigation/LOI)	AA [auth B], F [auth A], FB [auth D], PA [auth C], TB [auth E]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
LFA	BB [auth C], CB [auth C], DC [auth E], EC [auth E], FC [auth E], GA [auth B], GC [auth E], HA [auth B], HC [auth E], IA [auth B], IC [auth E], JA [auth B], JC [auth E], MA [auth B], NA [auth B], NB [auth D], OB [auth D], PB [auth D], QB [auth D], R [auth A], RB [auth D], S [auth A], SB [auth D], T [auth A], U [auth A], V [auth A], VB [auth E], W [auth A], WA [auth C], XA [auth C], Y [auth A], YA [auth C], ZA [auth C]	EICOSANE C20 H42 CBFCDTFDPHXCNY-UHFFFAOYSA-N
NA	BA [auth B], G [auth A], GB [auth D], QA [auth C], UB [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.1	α = 90
b = 240.9	β = 90
c = 138.5	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Zabelskii, D., Round, E., Han, H., von Stetten, D., Melo, D., de Wijn, R., Bean, R., Round, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release
  
• Version 1.1: 2025-11-26
  Changes: Database references