3X3B

Crystal structure of the light-driven sodium pump KR2 in acidic state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for Na(+) transport mechanism by a light-driven Na(+) pump

Kato, H.E.Inoue, K.Abe-Yoshizumi, R.Kato, Y.Ono, H.Konno, M.Hososhima, S.Ishizuka, T.Hoque, M.R.Kunitomo, H.Ito, J.Yoshizawa, S.Yamashita, K.Takemoto, M.Nishizawa, T.Taniguchi, R.Kogure, K.Maturana, A.D.Iino, Y.Yawo, H.Ishitani, R.Kandori, H.Nureki, O.

(2015) Nature 521: 48-53

  • DOI: 10.1038/nature14322
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Krokinobacter eikastus rhodopsin 2 (KR2) is the first light-driven Na(+) pump discovered, and is viewed as a potential next-generation optogenetics tool. Since the positively charged Schiff base proton, located within the ion-conducting pathway of al ...

    Krokinobacter eikastus rhodopsin 2 (KR2) is the first light-driven Na(+) pump discovered, and is viewed as a potential next-generation optogenetics tool. Since the positively charged Schiff base proton, located within the ion-conducting pathway of all light-driven ion pumps, was thought to prohibit the transport of a non-proton cation, the discovery of KR2 raised the question of how it achieves Na(+) transport. Here we present crystal structures of KR2 under neutral and acidic conditions, which represent the resting and M-like intermediate states, respectively. Structural and spectroscopic analyses revealed the gating mechanism, whereby the flipping of Asp116 sequesters the Schiff base proton from the conducting pathway to facilitate Na(+) transport. Together with the structure-based engineering of the first light-driven K(+) pumps, electrophysiological assays in mammalian neurons and behavioural assays in a nematode, our studies reveal the molecular basis for light-driven non-proton cation pumps and thus provide a framework that may advance the development of next-generation optogenetics.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium pumping rhodopsin
A
290Dokdonia eikastaGene Names: NaR
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
KR2 light-driven Na+ pump, acidic conditions
Find proteins for N0DKS8 (Dokdonia eikasta)
Go to UniProtKB:  N0DKS8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download SDF File 
Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
RET
Query on RET

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Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 40.582α = 90.00
b = 81.544β = 90.00
c = 233.775γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-05-13
    Type: Database references
  • Version 1.2: 2015-05-27
    Type: Structure summary