3X3B | pdb_00003x3b

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.249 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1038/nature14322
  • Primary Citation Related Structures: 
    3X3B, 3X3C

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 34.13 kDa 
  • Atom Count: 2,256 
  • Modeled Residue Count: 271 
  • Deposited Residue Count: 290 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium pumping rhodopsin290Dokdonia 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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.249 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.582α = 90
b = 81.544β = 90
c = 233.775γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2015-05-27
    Changes: Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary