6REX | pdb_00006rex

Crystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 6.0

PDB DOI: https://doi.org/10.2210/pdb6REX/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Dokdonia eikasta
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2019-04-12 Released: 2019-04-24
Deposition Author(s): Kovalev, K., Polovinkin, V., Gushchin, I., Borshchevskiy, V., Gordeliy, V.
Funding Organization(s): French National Research Agency, Russian Foundation for Basic Research, French Infrastructure for Integrated Structural Biology, Grenoble Alliance for Integrated Structural Cell Biology, Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.250 (Depositor), 0.256 (DCC)
R-Value Work:
0.223 (Depositor), 0.232 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 30989112 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.aav2671
Primary Citation Related Structures:
6REX, 6REZ, 6RF0, 6RF1, 6RF3, 6RF4, 6RF5, 6RF6, 6RF7, 6RF9, 6RFA, 6RFB, 6RFC

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. 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

Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.

Macromolecule Content

Total Structure Weight: 175.13 kDa
Atom Count: 12,192
Modeled Residue Count: 1,365
Deposited Residue Count: 1,365
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium pumping rhodopsin	A, B, C, D, E	273	Dokdonia eikasta	Mutation(s): 0 Gene Names: NaR Membrane Entity: Yes
UniProt
Find proteins for N0DKS8 (Dokdonia eikasta) Explore N0DKS8 Go to UniProtKB: N0DKS8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	N0DKS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain LB [auth E] SDF format, chain MA [auth C] SDF format, chain MB [auth E] SDF format, chain NB [auth E] SDF format, chain OB [auth E] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain XA [auth D] SDF format, chain YA [auth D] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth E] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth E] MOL2 format, chain NB [auth E] MOL2 format, chain OB [auth E] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth E] mmCIF format, chain MA [auth C] mmCIF format, chain MB [auth E] mmCIF format, chain NB [auth E] mmCIF format, chain OB [auth E] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth D]	AB [auth D] EA [auth C] F [auth A] FA [auth C] G [auth A] AB [auth D], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], IA [auth C], JA [auth C], KA [auth C], LA [auth C], LB [auth E], MA [auth C], MB [auth E], NB [auth E], OB [auth E], R [auth B], T [auth B], U [auth B], V [auth B], XA [auth D], YA [auth D], ZA [auth D]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain AB [auth D] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain OB [auth E] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain OB [auth E] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D]
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain JB [auth D] SDF format, chain O [auth A] SDF format, chain UA [auth C] SDF format, chain WB [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain WB [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain O [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain WB [auth E]	CA [auth B], JB [auth D], O [auth A], UA [auth C], WB [auth E]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain CA [auth B] Focus chain JB [auth D] Focus chain O [auth A] Focus chain UA [auth C] Focus chain WB [auth E] Interactions & Density Focus chain CA [auth B] Focus chain JB [auth D] Focus chain O [auth A] Focus chain UA [auth C] Focus chain WB [auth E]
RET Query on RET Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain KB [auth D] SDF format, chain Q [auth A] SDF format, chain VA [auth C] SDF format, chain ZB [auth E] MOL2 format, chain DA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain ZB [auth E] mmCIF format, chain DA [auth B] mmCIF format, chain KB [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain ZB [auth E]	DA [auth B], KB [auth D], Q [auth A], VA [auth C], ZB [auth E]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain DA [auth B] Focus chain KB [auth D] Focus chain Q [auth A] Focus chain VA [auth C] Focus chain ZB [auth E] Interactions & Density Focus chain DA [auth B] Focus chain KB [auth D] Focus chain Q [auth A] Focus chain VA [auth C] Focus chain ZB [auth E]
LFA Query on LFA Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain HA [auth C] SDF format, chain HB [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain PB [auth E] SDF format, chain QA [auth C] SDF format, chain QB [auth E] SDF format, chain RA [auth C] SDF format, chain RB [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth C] SDF format, chain SB [auth E] SDF format, chain TB [auth E] SDF format, chain UB [auth E] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XB [auth E] SDF format, chain Y [auth B] SDF format, chain YB [auth E] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain PB [auth E] MOL2 format, chain QA [auth C] MOL2 format, chain QB [auth E] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth E] MOL2 format, chain TB [auth E] MOL2 format, chain UB [auth E] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XB [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain YB [auth E] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain PB [auth E] mmCIF format, chain QA [auth C] mmCIF format, chain QB [auth E] mmCIF format, chain RA [auth C] mmCIF format, chain RB [auth E] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain SB [auth E] mmCIF format, chain TB [auth E] mmCIF format, chain UB [auth E] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XB [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain YB [auth E] mmCIF format, chain Z [auth B]	AA [auth B] BB [auth D] CB [auth D] DB [auth D] EB [auth D] AA [auth B], BB [auth D], CB [auth D], DB [auth D], EB [auth D], FB [auth D], GB [auth D], HA [auth C], HB [auth D], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], NA [auth C], OA [auth C], P [auth A], PA [auth C], PB [auth E], QA [auth C], QB [auth E], RA [auth C], RB [auth E], S [auth B], SA [auth C], SB [auth E], TB [auth E], UB [auth E], W [auth B], WA [auth D], X [auth B], XB [auth E], Y [auth B], YB [auth E], Z [auth B]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HA [auth C] Focus chain HB [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain S [auth B] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain TB [auth E] Focus chain UB [auth E] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XB [auth E] Focus chain Y [auth B] Focus chain YB [auth E] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HA [auth C] Focus chain HB [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain S [auth B] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain TB [auth E] Focus chain UB [auth E] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XB [auth E] Focus chain Y [auth B] Focus chain YB [auth E] Focus chain Z [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain IB [auth D] SDF format, chain N [auth A] SDF format, chain TA [auth C] SDF format, chain VB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain VB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain IB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain VB [auth E]	BA [auth B], IB [auth D], N [auth A], TA [auth C], VB [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain IB [auth D] Focus chain N [auth A] Focus chain TA [auth C] Focus chain VB [auth E] Interactions & Density Focus chain BA [auth B] Focus chain IB [auth D] Focus chain N [auth A] Focus chain TA [auth C] Focus chain VB [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.250 (Depositor), 0.256 (DCC)
R-Value Work: 0.223 (Depositor), 0.232 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.432	α = 90
b = 240.787	β = 90
c = 135.737	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-24

Deposition Author(s):

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-15-CE11-0029-02
Russian Foundation for Basic Research	Russian Federation	6.3157.2017/PP
French Infrastructure for Integrated Structural Biology	France	ANR-10-INSB-05-02
Grenoble Alliance for Integrated Structural Cell Biology	France	ANR-10-LABX-49-01
Russian Science Foundation	Russian Federation	RSF 16-15-00242

Revision History (Full details and data files)

Version 1.0: 2019-04-24
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Structure summary
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-10-23
Changes: Structure summary