6RF9

Crystal structure of the Y154F mutant of the light-driven sodium pump KR2 in the monomeric form, pH 8.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and mechanisms of sodium-pumping KR2 rhodopsin.

Kovalev, K.Polovinkin, V.Gushchin, I.Alekseev, A.Shevchenko, V.Borshchevskiy, V.Astashkin, R.Balandin, T.Bratanov, D.Vaganova, S.Popov, A.Chupin, V.Buldt, G.Bamberg, E.Gordeliy, V.

(2019) Sci Adv 5: eaav2671-eaav2671

  • DOI: 10.1126/sciadv.aav2671
  • Primary Citation of Related Structures:  
    6RFC, 6RFB, 6REZ, 6RFA, 6RF3, 6RF5, 6RF4, 6RF7, 6RF6, 6REX

  • PubMed Abstract: 
  • Rhodopsins are the most universal biological light-energy transducers and abundant phototrophic mechanisms that evolved on Earth and have a remarkable diversity and potential for biotechnological applications. Recently, the first sodium-pumping rhodopsin KR2 from Krokinobacter eikastus was discovered and characterized ...

    Rhodopsins are the most universal biological light-energy transducers and abundant phototrophic mechanisms that evolved on Earth and have a remarkable diversity and potential for biotechnological applications. Recently, the first sodium-pumping rhodopsin KR2 from Krokinobacter eikastus was discovered and characterized. However, the existing structures of KR2 are contradictory, and the mechanism of Na + pumping is not yet understood. Here, we present a structure of the cationic (non H + ) light-driven pump at physiological pH in its pentameric form. We also present 13 atomic structures and functional data on the KR2 and its mutants, including potassium pumps, which show that oligomerization of the microbial rhodopsin is obligatory for its biological function. The studies reveal the structure of KR2 at nonphysiological low pH where it acts as a proton pump. The structure provides new insights into the mechanisms of microbial rhodopsins and opens the way to a rational design of novel cation pumps for optogenetics.


    Organizational Affiliation

    Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium pumping rhodopsinA288Dokdonia eikastaMutation(s): 1 
Gene Names: NaR
Membrane Entity: Yes 
UniProt
Find proteins for N0DKS8 (Dokdonia eikasta)
Explore N0DKS8 
Go to UniProtKB:  N0DKS8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

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

Download Ideal Coordinates CCD File 
B [auth A] , C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [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],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  R [auth A],  S [auth A],  T [auth A],  V [auth A],  W [auth A]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A], P [auth A], Q [auth A], U [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.472α = 90
b = 81.851β = 90
c = 233.57γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE11-0029-02
Russian Foundation for Basic ResearchRussian Federation6.3157.2017/PP
French Infrastructure for Integrated Structural BiologyFranceANR-10-INSB-05-02
Grenoble Alliance for Integrated Structural Cell BiologyFranceANR-10-LABX-49-01
Russian Science FoundationRussian FederationRSF 16-15-00242

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Refinement description