7Q36

Crystal structure of KR2 sodium pump rhodopsin pressurized with krypton


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action.

Melnikov, I.Orekhov, P.Rulev, M.Kovalev, K.Astashkin, R.Bratanov, D.Ryzhykau, Y.Balandin, T.Bukhdruker, S.Okhrimenko, I.Borshchevskiy, V.Bourenkov, G.Mueller-Dieckmann, C.van der Linden, P.Carpentier, P.Leonard, G.Gordeliy, V.Popov, A.

(2022) Commun Biol 5: 360-360

  • DOI: https://doi.org/10.1038/s42003-022-03233-y
  • Primary Citation of Related Structures:  
    7Q35, 7Q36, 7Q37, 7Q38

  • PubMed Abstract: 

    In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs - a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia.


  • Organizational Affiliation

    Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium pumping rhodopsin280Dokdonia eikastaMutation(s): 0 
Gene Names: NaR
Membrane Entity: Yes 
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download Ideal Coordinates CCD File 
PA [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
HEX
Query on HEX

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
CA [auth A],
Y [auth A],
Z [auth A]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
KR (Subject of Investigation/LOI)
Query on KR

Download Ideal Coordinates CCD File 
EA [auth A]
FA [auth A]
GA [auth A]
HA [auth A]
IA [auth A]
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A]
KRYPTON
Kr
DNNSSWSSYDEUBZ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.489α = 90
b = 82.18β = 90
c = 233.442γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description