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 1.0 of the entry. See complete history.

Literature

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

Gemin, O., Armijo, V., Papp, G.

To be published.

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

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 GB [auth D] SDF format, chain MA [auth C] SDF format, chain RA [auth C] SDF format, chain X [auth B] MOL2 format, chain F [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain X [auth B] mmCIF format, chain F [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain MA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain X [auth B]	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 AC [auth E] SDF format, chain H [auth A] SDF format, chain HB [auth D] SDF format, chain OA [auth C] SDF format, chain Y [auth B] MOL2 format, chain AC [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain OA [auth C] MOL2 format, chain Y [auth B] mmCIF format, chain AC [auth E] mmCIF format, chain H [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain OA [auth C] mmCIF format, chain Y [auth B]	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 CA [auth B] SDF format, chain CB [auth C] SDF format, chain CC [auth E] SDF format, chain DA [auth B] 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 G [auth A] 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 IA [auth B] SDF format, chain IC [auth E] SDF format, chain JA [auth B] 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 L [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth D] SDF format, chain LC [auth E] SDF format, chain M [auth A] SDF format, chain MB [auth D] SDF format, chain N [auth A] 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 SB [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain TB [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain UB [auth D] SDF format, chain VA [auth C] SDF format, chain VB [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth C] SDF format, chain WB [auth E] SDF format, chain XA [auth C] SDF format, chain XB [auth E] SDF format, chain YA [auth C] SDF format, chain YB [auth E] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] SDF format, chain ZB [auth E] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain CC [auth E] MOL2 format, chain DA [auth B] 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 G [auth A] 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 IA [auth B] MOL2 format, chain IC [auth E] MOL2 format, chain JA [auth B] 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 L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth D] MOL2 format, chain LC [auth E] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain N [auth A] 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 SB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain UB [auth D] MOL2 format, chain VA [auth C] MOL2 format, chain VB [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain WB [auth E] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth E] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth E] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain CC [auth E] mmCIF format, chain DA [auth B] 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 G [auth A] 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 IA [auth B] mmCIF format, chain IC [auth E] mmCIF format, chain JA [auth B] 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 L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth D] mmCIF format, chain LC [auth E] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain N [auth A] 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 SB [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain TB [auth D] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain UB [auth D] mmCIF format, chain VA [auth C] mmCIF format, chain VB [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain WB [auth E] mmCIF format, chain XA [auth C] mmCIF format, chain XB [auth E] mmCIF format, chain YA [auth C] mmCIF format, chain YB [auth E] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain ZB [auth E]	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 EB [auth D] SDF format, chain EC [auth E] SDF format, chain J [auth A] SDF format, chain V [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain EC [auth E] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain EC [auth E] mmCIF format, chain J [auth A] mmCIF format, chain V [auth B]	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]