6YC0

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

  • Method: X-RAY DIFFRACTION
  • 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 1.1 of the entry. See complete history


Literature

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: 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 ...

    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

    Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia. valentin.gordeliy@ibs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium pumping rhodopsinA, B, C, D, E273Dokdonia 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
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
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
RET
Query on RET

Download Ideal Coordinates CCD File 
AC [auth E],
EA [auth B],
JB [auth D],
T [auth A],
WA [auth C]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
LFA
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]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
OLA
Query on OLA

Download Ideal Coordinates CCD File 
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]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
GOL
Query on GOL

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.21α = 90
b = 240.34β = 90
c = 138.37γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report




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