Crystal structure of the steady-state-SMX activated state of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Molecular mechanism of light-driven sodium pumping.

Kovalev, K.Astashkin, R.Gushchin, I.Orekhov, P.Volkov, D.Zinovev, E.Marin, E.Rulev, M.Alekseev, A.Royant, A.Carpentier, P.Vaganova, S.Zabelskii, D.Baeken, C.Sergeev, I.Balandin, T.Bourenkov, G.Carpena, X.Boer, R.Maliar, N.Borshchevskiy, V.Buldt, G.Bamberg, E.Gordeliy, V.

(2020) Nat Commun 11: 2137-2137

  • DOI: https://doi.org/10.1038/s41467-020-16032-y
  • Primary Citation of Related Structures:  
    6XYT, 6YBY, 6YBZ, 6YC0, 6YC1, 6YC2, 6YC3, 6YC4

  • PubMed Abstract: 

    The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 Å, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools.

  • Organizational Affiliation

    JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium pumping rhodopsin
A, B, C, D, E
273Dokdonia eikastaMutation(s): 0 
Gene Names: NaR
Membrane Entity: Yes 
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
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OLC

Download Ideal Coordinates CCD File 
AB [auth D]
BB [auth D]
CB [auth D]
F [auth A]
G [auth A]
AB [auth D],
BB [auth D],
CB [auth D],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
JA [auth C],
KA [auth C],
KB [auth D],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
PA [auth C],
QB [auth E],
R [auth A],
RB [auth E],
S [auth A],
SB [auth E],
TB [auth E],
U [auth A],
X [auth B],
XA [auth C],
Y [auth B],
Z [auth B],
ZA [auth D]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on RET

Download Ideal Coordinates CCD File 
AC [auth E],
EA [auth B],
JB [auth D],
T [auth A],
WA [auth C]
C20 H28 O
Query on LFA

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DB [auth D]
EB [auth D]
AA [auth B],
BA [auth B],
CA [auth B],
DB [auth D],
EB [auth D],
FB [auth D],
GB [auth D],
HB [auth D],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
QA [auth C],
RA [auth C],
SA [auth C],
UB [auth E],
VB [auth E],
WB [auth E],
XB [auth E]
C20 H42
Query on OLA

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FA [auth B]
GA [auth B]
LB [auth D]
NB [auth E]
OB [auth E]
FA [auth B],
GA [auth B],
LB [auth D],
NB [auth E],
OB [auth E],
PB [auth E],
UA [auth C],
ZB [auth E]
C18 H34 O2
Query on GOL

Download Ideal Coordinates CCD File 
HA [auth B],
V [auth A],
VA [auth C]
C3 H8 O3
NA (Subject of Investigation/LOI)
Query on NA

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BC [auth E]
DA [auth B]
IA [auth B]
IB [auth D]
MB [auth D]
BC [auth E],
DA [auth B],
IA [auth B],
IB [auth D],
MB [auth D],
Q [auth A],
TA [auth C],
W [auth A],
YA [auth C],
YB [auth E]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.21α = 90
b = 240.34β = 90
c = 138.37γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
CrystFELdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE11-0029-02
French National Research AgencyFranceANR-10-INBS-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR-17-EURE-0003
Russian Science FoundationRussian Federation16-15-00242
Russian Science FoundationRussian Federation6.3157.2017/PP

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-01-24
    Changes: Refinement description