8RQ5 | pdb_00008rq5

Cryo-EM structure of the light-driven sodium-pumping rhodopsin KR2

PDB DOI: https://doi.org/10.2210/pdb8RQ5/pdb
EM Map EMD-19434: EMDB EMDataResource

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

Deposited: 2024-01-17 Released: 2025-01-29
Deposition Author(s): Kovalev, K., Linares, R.
Funding Organization(s): EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control.

Gemin, O., Armijo, V., Lecomte, L., Hons, M., Deckers, T., Bissardon, C., Rossi, C., Lauzier, K., Janocha, R., Felisaz, F., Sinoir, J., Linares, R., Babenko, A., Kovalev, K., Prokhorova, I., Khusainov, I., Schreiner, C., Kolesnikova, O., Salo, V.T., Schneider, S., Bowler, M.W., Wolff, G., Galej, W.P., Mahamid, J., Muller, C.W., Carugo, K.D., Eustermann, S., Mattei, S., Cipriani, F., Papp, G.

(2026) Nat Methods

PubMed: 42337080 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41592-026-03127-5
Primary Citation Related Structures:
8RQ5

PubMed Abstract:
Optimized sample preparation is essential for imaging biological macromolecules in their native state using single-particle cryo-electron microscopy (cryo-EM) or in situ cryo-electron tomography (cryo-ET). Here we present EasyGrid, a modular, automated platform designed to streamline and standardize cryo-EM/ET sample preparation. EasyGrid integrates in-line plasma treatment of the sample support, microfluidic dispensing, blot-less sample spreading, jet-based vitrification and grid quality control via light interferometry. We demonstrate its effectiveness by preparing grids for multiple purified macromolecular complexes and resolving their structures with cryo-EM. Additionally, EasyGrid achieves improved vitrification of large mammalian cells compared to conventional plunge-freezing. By enabling systematic and high-throughput optimization, EasyGrid provides a robust and time-saving solution for both structural and cellular cryo-EM applications.

Organizational Affiliation

Molecular Systems Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 180.8 kDa
Atom Count: 12,137
Modeled Residue Count: 1,340
Deposited Residue Count: 1,400
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	280	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 F [auth A] SDF format, chain MA [auth C] SDF format, chain RA [auth C] SDF format, chain X [auth B] SDF format, chain GB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain GB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain GB [auth D]	F [auth A], GB [auth D], MA [auth C], RA [auth C], X [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain F [auth A] Focus chain GB [auth D] Focus chain MA [auth C] Focus chain RA [auth C] Focus chain X [auth B] Interactions & Density Focus chain F [auth A] Focus chain GB [auth D] Focus chain MA [auth C] Focus chain RA [auth C] Focus chain X [auth B]
RET (Subject of Investigation/LOI) Query on RET Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain OA [auth C] SDF format, chain Y [auth B] SDF format, chain HB [auth D] SDF format, chain AC [auth E] MOL2 format, chain H [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain AC [auth E] mmCIF format, chain H [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain AC [auth E]	AC [auth E], H [auth A], HB [auth D], OA [auth C], Y [auth B]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain AC [auth E] Focus chain H [auth A] Focus chain HB [auth D] Focus chain OA [auth C] Focus chain Y [auth B] Interactions & Density Focus chain AC [auth E] Focus chain H [auth A] Focus chain HB [auth D] Focus chain OA [auth C] Focus chain Y [auth B]
LFA Query on LFA Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CC [auth E] SDF format, chain DB [auth C] SDF format, chain DC [auth E] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain FC [auth E] SDF format, chain GA [auth B] SDF format, chain GC [auth E] SDF format, chain HA [auth B] SDF format, chain HC [auth E] SDF format, chain JB [auth D] SDF format, chain JC [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth D] SDF format, chain KC [auth E] SDF format, chain LA [auth B] SDF format, chain LB [auth D] SDF format, chain LC [auth E] SDF format, chain NA [auth C] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RB [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain VA [auth C] SDF format, chain VB [auth D] SDF format, chain W [auth B] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] SDF format, chain ZB [auth E] SDF format, chain YB [auth E] SDF format, chain XB [auth E] SDF format, chain WB [auth E] SDF format, chain WA [auth C] SDF format, chain UB [auth D] SDF format, chain UA [auth C] SDF format, chain TB [auth D] SDF format, chain T [auth A] SDF format, chain SB [auth D] SDF format, chain N [auth A] SDF format, chain MB [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain JA [auth B] SDF format, chain IC [auth E] SDF format, chain IA [auth B] SDF format, chain G [auth A] SDF format, chain DA [auth B] SDF format, chain CB [auth C] SDF format, chain CA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CC [auth E] MOL2 format, chain DB [auth C] MOL2 format, chain DC [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain FC [auth E] MOL2 format, chain GA [auth B] MOL2 format, chain GC [auth E] MOL2 format, chain HA [auth B] MOL2 format, chain HC [auth E] MOL2 format, chain JB [auth D] MOL2 format, chain JC [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain KC [auth E] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth D] MOL2 format, chain LC [auth E] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain VB [auth D] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth E] MOL2 format, chain YB [auth E] MOL2 format, chain XB [auth E] MOL2 format, chain WB [auth E] MOL2 format, chain WA [auth C] MOL2 format, chain UB [auth D] MOL2 format, chain UA [auth C] MOL2 format, chain TB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain SB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain IC [auth E] MOL2 format, chain IA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain CA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CC [auth E] mmCIF format, chain DB [auth C] mmCIF format, chain DC [auth E] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain FC [auth E] mmCIF format, chain GA [auth B] mmCIF format, chain GC [auth E] mmCIF format, chain HA [auth B] mmCIF format, chain HC [auth E] mmCIF format, chain JB [auth D] mmCIF format, chain JC [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth D] mmCIF format, chain KC [auth E] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth D] mmCIF format, chain LC [auth E] mmCIF format, chain NA [auth C] mmCIF format, chain NB [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain QB [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth D] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain VB [auth D] mmCIF format, chain W [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain ZB [auth E] mmCIF format, chain YB [auth E] mmCIF format, chain XB [auth E] mmCIF format, chain WB [auth E] mmCIF format, chain WA [auth C] mmCIF format, chain UB [auth D] mmCIF format, chain UA [auth C] mmCIF format, chain TB [auth D] mmCIF format, chain T [auth A] mmCIF format, chain SB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain IC [auth E] mmCIF format, chain IA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain CA [auth B]	AB [auth C] BA [auth B] BB [auth C] CA [auth B] CB [auth C] AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], CC [auth E], DA [auth B], DB [auth C], DC [auth E], EA [auth B], FA [auth B], FB [auth D], FC [auth E], G [auth A], GA [auth B], GC [auth E], HA [auth B], HC [auth E], IA [auth B], IC [auth E], JA [auth B], JB [auth D], JC [auth E], K [auth A], KA [auth B], KB [auth D], KC [auth E], L [auth A], LA [auth B], LB [auth D], LC [auth E], M [auth A], MB [auth D], N [auth A], NA [auth C], NB [auth D], O [auth A], OB [auth D], P [auth A], PB [auth D], Q [auth A], QA [auth C], QB [auth D], R [auth A], RB [auth D], S [auth A], SA [auth C], SB [auth D], T [auth A], TA [auth C], TB [auth D], U [auth A], UA [auth C], UB [auth D], VA [auth C], VB [auth D], W [auth B], WA [auth C], WB [auth E], XA [auth C], XB [auth E], YA [auth C], YB [auth E], Z [auth B], ZA [auth C], ZB [auth E]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain CC [auth E] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain DC [auth E] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FC [auth E] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GC [auth E] Focus chain HA [auth B] Focus chain HC [auth E] Focus chain IA [auth B] Focus chain IC [auth E] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain JC [auth E] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain KC [auth E] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain LC [auth E] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain VA [auth C] Focus chain VB [auth D] Focus chain W [auth B] Focus chain WA [auth C] Focus chain WB [auth E] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain Z [auth B] Focus chain ZA [auth C] Focus chain ZB [auth E] Interactions & Density Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain CC [auth E] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain DC [auth E] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FC [auth E] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GC [auth E] Focus chain HA [auth B] Focus chain HC [auth E] Focus chain IA [auth B] Focus chain IC [auth E] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain JC [auth E] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain KC [auth E] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain LC [auth E] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain VA [auth C] Focus chain VB [auth D] Focus chain W [auth B] Focus chain WA [auth C] Focus chain WB [auth E] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain Z [auth B] Focus chain ZA [auth C] Focus chain ZB [auth E]
OLA Query on OLA Download:Ideal Coordinates CCD File SDF format, chain EC [auth E] SDF format, chain J [auth A] SDF format, chain V [auth B] SDF format, chain EB [auth D] MOL2 format, chain EC [auth E] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B] MOL2 format, chain EB [auth D] mmCIF format, chain EC [auth E] mmCIF format, chain J [auth A] mmCIF format, chain V [auth B] mmCIF format, chain EB [auth D]	EB [auth D], EC [auth E], J [auth A], V [auth B]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain EB [auth D] Focus chain EC [auth E] Focus chain J [auth A] Focus chain V [auth B] Interactions & Density Focus chain EB [auth D] Focus chain EC [auth E] Focus chain J [auth A] Focus chain V [auth B]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BC [auth E] SDF format, chain I [auth A] SDF format, chain IB [auth D] SDF format, chain PA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BC [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain PA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain BC [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain PA [auth C]	AA [auth B], BC [auth E], I [auth A], IB [auth D], PA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BC [auth E] Focus chain I [auth A] Focus chain IB [auth D] Focus chain PA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain BC [auth E] Focus chain I [auth A] Focus chain IB [auth D] Focus chain PA [auth C]