6EYU

Crystal structure of the inward H(+) pump xenorhodopsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inward H(+) pump xenorhodopsin: Mechanism and alternative optogenetic approach.

Shevchenko, V.Mager, T.Kovalev, K.Polovinkin, V.Alekseev, A.Juettner, J.Chizhov, I.Bamann, C.Vavourakis, C.Ghai, R.Gushchin, I.Borshchevskiy, V.Rogachev, A.Melnikov, I.Popov, A.Balandin, T.Rodriguez-Valera, F.Manstein, D.J.Bueldt, G.Bamberg, E.Gordeliy, V.

(2017) Sci Adv 3: e1603187

  • DOI: 10.1126/sciadv.1603187

  • PubMed Abstract: 
  • Generation of an electrochemical proton gradient is the first step of cell bioenergetics. In prokaryotes, the gradient is created by outward membrane protein proton pumps. Inward plasma membrane native proton pumps are yet unknown. We describe compre ...

    Generation of an electrochemical proton gradient is the first step of cell bioenergetics. In prokaryotes, the gradient is created by outward membrane protein proton pumps. Inward plasma membrane native proton pumps are yet unknown. We describe comprehensive functional studies of the representatives of the yet noncharacterized xenorhodopsins from Nanohaloarchaea family of microbial rhodopsins. They are inward proton pumps as we demonstrate in model membrane systems, Escherichia coli cells, human embryonic kidney cells, neuroblastoma cells, and rat hippocampal neuronal cells. We also solved the structure of a xenorhodopsin from the nanohalosarchaeon Nanosalina (NsXeR) and suggest a mechanism of inward proton pumping. We demonstrate that the NsXeR is a powerful pump, which is able to elicit action potentials in rat hippocampal neuronal cells up to their maximal intrinsic firing frequency. Hence, inwardly directed proton pumps are suitable for light-induced remote control of neurons, and they are an alternative to the well-known cation-selective channelrhodopsins.


    Organizational Affiliation

    Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriorhodopsin
A, B, C
232Nanosalina sp. (strain J07AB43)Mutation(s): 0 
Find proteins for G0QG75 (Nanosalina sp. (strain J07AB43))
Go to UniProtKB:  G0QG75
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download SDF File 
Download CCD File 
A, B, C
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
LFA
Query on LFA

Download SDF File 
Download CCD File 
A, B, C
EICOSANE
LIPID FRAGMENT
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
MUN
Query on MUN

Download SDF File 
Download CCD File 
A, B, C
[(2~{S})-2,3-bis(oxidanyl)propyl] (~{E})-undec-2-enoate
MONOUNDECENOIN
C14 H26 O4
INMIULFREHIAOX-LXKVQUBZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.010α = 90.00
b = 93.870β = 90.00
c = 196.210γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE11-0029-02
German Research FoundationGermanyANR-15-CE11-0029-02
French Infrastructure for Integrated Structural BiologyFranceANR-10-INSB-05-02
GRAFranceANR-10-LABX-49-01
ERA.Net RUS PLUS and Ministry of Education and Science of the Russian FederationRussian FederationID 323, RFMEFI58715X0011

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-31
    Type: Advisory, Author supporting evidence, Derived calculations, Structure summary