4XTO

Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 5.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of a light-driven sodium pump.

Gushchin, I.Shevchenko, V.Polovinkin, V.Kovalev, K.Alekseev, A.Round, E.Borshchevskiy, V.Balandin, T.Popov, A.Gensch, T.Fahlke, C.Bamann, C.Willbold, D.Buldt, G.Bamberg, E.Gordeliy, V.

(2015) Nat.Struct.Mol.Biol. 22: 390-395

  • DOI: 10.1038/nsmb.3002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recently, the first known light-driven sodium pumps, from the microbial rhodopsin family, were discovered. We have solved the structure of one of them, Krokinobacter eikastus rhodopsin 2 (KR2), in the monomeric blue state and in two pentameric red st ...

    Recently, the first known light-driven sodium pumps, from the microbial rhodopsin family, were discovered. We have solved the structure of one of them, Krokinobacter eikastus rhodopsin 2 (KR2), in the monomeric blue state and in two pentameric red states, at resolutions of 1.45 Å and 2.2 and 2.8 Å, respectively. The structures reveal the ion-translocation pathway and show that the sodium ion is bound outside the protein at the oligomerization interface, that the ion-release cavity is capped by a unique N-terminal α-helix and that the ion-uptake cavity is unexpectedly large and open to the surface. Obstruction of the cavity with the mutation G263F imparts KR2 with the ability to pump potassium. These results pave the way for the understanding and rational design of cation pumps with new specific properties valuable for optogenetics.


    Organizational Affiliation

    1] Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France. [2] Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Grenoble, France. [3] Institut de Biologie Structurale, Commissariat à l'Énergie Atomique (CEA), Grenoble, France. [4] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [5] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium pumping rhodopsin
A, B, C, D, E
288Dokdonia eikastaMutation(s): 0 
Gene Names: NaR
Find proteins for N0DKS8 (Dokdonia eikasta)
Go to UniProtKB:  N0DKS8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LFA
Query on LFA

Download SDF File 
Download CCD File 
A, B, C, D, E
EICOSANE
LIPID FRAGMENT
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LYR
Query on LYR
A, B, C, D, E
L-PEPTIDE LINKINGC26 H42 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 127.100α = 90.00
b = 238.980β = 90.00
c = 132.480γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Database references
  • Version 1.2: 2015-04-22
    Type: Database references
  • Version 1.3: 2015-04-29
    Type: Database references
  • Version 1.4: 2015-05-13
    Type: Database references