9I6I | pdb_00009i6i

Room-temperature structure of KR2 rhodopsin in pentameric form at 85% relative humidity

PDB DOI: https://doi.org/10.2210/pdb9I6I/pdb

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

Deposited: 2025-01-30 Released: 2025-07-16
Deposition Author(s): Zabelskii, D., Round, E., Han, H., von Stetten, D., Melo, D., de Wijn, R., Bean, R., Round, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.197 (Depositor), 0.197 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Viscoelastic characterization of the lipid cubic phase provides insights into high-viscosity extrusion injection for XFEL experiments.

Zabelskii, D., Round, E., Han, H., von Stetten, D., Letrun, R., Kim, C., Sato, T., Melo, D., de Wijn, R., Kharitonov, K., Smyth, P., Doerner, K., Kloos, M., Dietze, T., Lopez, L., Bean, R., Round, A.

To be published.

Macromolecule Content

Total Structure Weight: 179.87 kDa
Atom Count: 11,932
Modeled Residue Count: 1,343
Deposited Residue Count: 1,365
Unique protein chains: 1

Macromolecules

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