9I6I | pdb_00009i6i

Room-temperature structure of KR2 rhodopsin in pentameric form at 85% relative humidity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41598-025-25449-8
  • Primary Citation of 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.


  • Organizational Affiliation
    • European XFEL GmbH, Schenefeld, Germany. dmitrii.zabelskii@xfel.eu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium pumping rhodopsin
A, B, C, D, E
273Dokdonia eikastaMutation(s): 0 
Gene Names: NaR
UniProt
Find proteins for N0DKS8 (Dokdonia eikasta)
Explore N0DKS8 
Go to UniProtKB:  N0DKS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN0DKS8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
AA [auth B]
AC [auth E]
BA [auth B]
BB [auth C]
BC [auth E]
AA [auth B],
AC [auth E],
BA [auth B],
BB [auth C],
BC [auth E],
CA [auth B],
CB [auth C],
DA [auth B],
EA [auth B],
FB [auth D],
GB [auth D],
H [auth A],
HB [auth D],
I [auth A],
IB [auth D],
J [auth A],
JA [auth B],
JB [auth D],
JC [auth E],
K [auth A],
KB [auth D],
KC [auth E],
L [auth A],
LB [auth D],
LC [auth E],
M [auth A],
MA [auth B],
MB [auth D],
N [auth A],
O [auth A],
P [auth A],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
WB [auth E],
X [auth A],
XB [auth E],
YA [auth C],
YB [auth E],
ZB [auth E]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
DB [auth D],
F [auth A],
NA [auth C],
TB [auth E],
Y [auth B]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
AB [auth C]
CC [auth E]
DC [auth E]
EC [auth E]
FA [auth B]
AB [auth C],
CC [auth E],
DC [auth E],
EC [auth E],
FA [auth B],
FC [auth E],
GA [auth B],
GC [auth E],
HA [auth B],
HC [auth E],
IA [auth B],
IC [auth E],
KA [auth B],
LA [auth B],
NB [auth D],
OB [auth D],
PB [auth D],
Q [auth A],
QB [auth D],
R [auth A],
RB [auth D],
S [auth A],
SB [auth D],
T [auth A],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
VB [auth E],
W [auth A],
WA [auth C],
XA [auth C],
ZA [auth C]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
EB [auth D],
G [auth A],
OA [auth C],
UB [auth E],
Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.1α = 90
b = 240.9β = 90
c = 138.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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