9I6H | pdb_00009i6h

Room temperature structure of KR2 rhodopsin in pentameric form at 95% relative humidity

PDB DOI: https://doi.org/10.2210/pdb9I6H/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:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (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: 11,939
Modeled Residue Count: 1,342
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 AB [auth C] SDF format, chain AC [auth E] SDF format, chain BC [auth E] SDF format, chain CA [auth B] SDF format, chain CC [auth E] SDF format, chain DA [auth B] SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] 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 JB [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth B] 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 O [auth A] SDF format, chain OA [auth B] SDF format, chain Q [auth A] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain X [auth A] SDF format, chain XB [auth E] SDF format, chain YB [auth E] SDF format, chain ZB [auth E] SDF format, chain KB [auth D] SDF format, chain KC [auth E] SDF format, chain P [auth A] SDF format, chain TA [auth C] SDF format, chain WB [auth E] SDF format, chain Z [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain AC [auth E] MOL2 format, chain BC [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain CC [auth E] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] 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 JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] 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 O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XB [auth E] MOL2 format, chain YB [auth E] MOL2 format, chain ZB [auth E] MOL2 format, chain KB [auth D] MOL2 format, chain KC [auth E] MOL2 format, chain P [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain WB [auth E] MOL2 format, chain Z [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain AC [auth E] mmCIF format, chain BC [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain CC [auth E] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth B] 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 JB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] 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 O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XB [auth E] mmCIF format, chain YB [auth E] mmCIF format, chain ZB [auth E] mmCIF format, chain KB [auth D] mmCIF format, chain KC [auth E] mmCIF format, chain P [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain WB [auth E] mmCIF format, chain Z [auth A]	AB [auth C] AC [auth E] BC [auth E] CA [auth B] CC [auth E] AB [auth C], AC [auth E], BC [auth E], CA [auth B], CC [auth E], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], H [auth A], HB [auth D], I [auth A], IB [auth D], J [auth A], JB [auth D], 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], O [auth A], OA [auth B], P [auth A], Q [auth A], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WB [auth E], X [auth A], XB [auth E], YB [auth E], Z [auth A], ZB [auth E]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain AB [auth C] Focus chain AC [auth E] Focus chain BC [auth E] Focus chain CA [auth B] Focus chain CC [auth E] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] 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 JB [auth D] 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 O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WB [auth E] Focus chain X [auth A] Focus chain XB [auth E] Focus chain YB [auth E] Focus chain Z [auth A] Focus chain ZB [auth E] Interactions & Density Focus chain AB [auth C] Focus chain AC [auth E] Focus chain BC [auth E] Focus chain CA [auth B] Focus chain CC [auth E] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] 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 JB [auth D] 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 O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WB [auth E] Focus chain X [auth A] Focus chain XB [auth E] Focus chain YB [auth E] Focus chain Z [auth A] Focus chain ZB [auth E]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain F [auth A] SDF format, chain FB [auth D] SDF format, chain TB [auth E] SDF format, chain PA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain TB [auth E] MOL2 format, chain PA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain TB [auth E] mmCIF format, chain PA [auth C]	AA [auth B], F [auth A], FB [auth D], PA [auth C], TB [auth E]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain AA [auth B] Focus chain F [auth A] Focus chain FB [auth D] Focus chain PA [auth C] Focus chain TB [auth E] Interactions & Density Focus chain AA [auth B] Focus chain F [auth A] Focus chain FB [auth D] Focus chain PA [auth C] Focus chain TB [auth E]
LFA Query on LFA Download Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DC [auth E] SDF format, chain EC [auth E] 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 JA [auth B] SDF format, chain JC [auth E] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain OB [auth D] SDF format, chain PB [auth D] 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 V [auth A] 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 Y [auth A] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DC [auth E] MOL2 format, chain EC [auth E] 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 JA [auth B] MOL2 format, chain JC [auth E] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain OB [auth D] MOL2 format, chain PB [auth D] 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 V [auth A] 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 Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DC [auth E] mmCIF format, chain EC [auth E] 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 JA [auth B] mmCIF format, chain JC [auth E] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth D] mmCIF format, chain OB [auth D] mmCIF format, chain PB [auth D] 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 V [auth A] 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 Y [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	BB [auth C] CB [auth C] DC [auth E] EC [auth E] FC [auth E] BB [auth C], CB [auth C], DC [auth E], EC [auth E], FC [auth E], GA [auth B], GC [auth E], HA [auth B], HC [auth E], IA [auth B], IC [auth E], JA [auth B], JC [auth E], MA [auth B], NA [auth B], NB [auth D], OB [auth D], PB [auth D], QB [auth D], R [auth A], RB [auth D], S [auth A], SB [auth D], T [auth A], U [auth A], V [auth A], VB [auth E], W [auth A], WA [auth C], XA [auth C], Y [auth A], YA [auth C], ZA [auth C]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DC [auth E] Focus chain EC [auth E] 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 JA [auth B] Focus chain JC [auth E] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] 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 V [auth A] Focus chain VB [auth E] Focus chain W [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DC [auth E] Focus chain EC [auth E] 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 JA [auth B] Focus chain JC [auth E] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] 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 V [auth A] Focus chain VB [auth E] Focus chain W [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain ZA [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain G [auth A] SDF format, chain GB [auth D] SDF format, chain QA [auth C] SDF format, chain UB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain QA [auth C] MOL2 format, chain UB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain QA [auth C] mmCIF format, chain UB [auth E]	BA [auth B], G [auth A], GB [auth D], QA [auth C], UB [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain G [auth A] Focus chain GB [auth D] Focus chain QA [auth C] Focus chain UB [auth E] Interactions & Density Focus chain BA [auth B] Focus chain G [auth A] Focus chain GB [auth D] Focus chain QA [auth C] Focus chain UB [auth E]