6EYU

Crystal structure of the inward H(+) pump xenorhodopsin

• PDB DOI:  https://doi.org/10.2210/pdb6EYU/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Candidatus Nanosalina sp. J07AB43
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-13 Released: 2017-12-13 
• Deposition Author(s): Kovalev, K., Shevchenko, V., Polovinkin, V., Mager, T., Gushchin, I., Melnikov, I., Borshchevskiy, V., Popov, A., Alekseev, A., Gordeliy, V.
• Funding Organization(s): French National Research Agency, German Research Foundation, French Infrastructure for Integrated Structural Biology, GRA, ERA.Net RUS PLUS and Ministry of Education and Science of the Russian Federation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.254 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

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

• PubMed: 28948217 
• DOI: https://doi.org/10.1126/sciadv.1603187
• Primary Citation of Related Structures:  
  6EYU


• 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 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 ( Ns XeR) and suggest a mechanism of inward proton pumping. We demonstrate that the Ns XeR 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: 

Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 88.52 kDa 
• Atom Count: 6,046 
• Modelled Residue Count: 693 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A, B, C	232	Candidatus Nanosalina sp. J07AB43	Mutation(s): 0  Gene Names: J07AB43_12860

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	D [auth A], HA [auth C], X [auth B]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
LFA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], IA [auth C], J [auth A], JA [auth C], KA [auth C], LA [auth C], MA [auth C], Y [auth B]	EICOSANE C20 H42 CBFCDTFDPHXCNY-UHFFFAOYSA-N
MUN	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], Z [auth B]	[(2~{S})-2,3-bis(oxidanyl)propyl] (~{E})-undec-2-enoate C14 H26 O4 INMIULFREHIAOX-LXKVQUBZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.254 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.01	α = 90
b = 93.87	β = 90
c = 196.21	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-13 
Deposition Author(s): Kovalev, K., Shevchenko, V., Polovinkin, V., Mager, T., Gushchin, I., Melnikov, I., Borshchevskiy, V., Popov, A., Alekseev, A., Gordeliy, V.

---

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-15-CE11-0029-02
German Research Foundation	Germany	ANR-15-CE11-0029-02
French Infrastructure for Integrated Structural Biology	France	ANR-10-INSB-05-02
GRA	France	ANR-10-LABX-49-01
ERA.Net RUS PLUS and Ministry of Education and Science of the Russian Federation	Russian Federation	ID 323, RFMEFI58715X0011

Revision History  

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