8RSO | pdb_00008rso

Crystal structure of marine actinobacteria clade rhodopsin (MAR) in the ground state

PDB DOI: https://doi.org/10.2210/pdb8RSO/pdb

Classification: MEMBRANE PROTEIN
Organism(s): marine Actinobacteria clade
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-25 Released: 2025-04-02
Deposition Author(s): Bukhdruker, S., Kovalev, K., Astashkin, R., Gordeliy, V.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 ?
R-Value Free:
0.177 (Depositor), 0.176 (DCC)
R-Value Work:
0.151 (Depositor), 0.152 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Proteorhodopsin Insights into Molecular Mechanism of Vectorial Proton Transport

Shevchenko, V., Gushchin, I., Polovinkin, V., Kovalev, K.

(2025) Sci Adv

Macromolecule Content

Total Structure Weight: 57.3 kDa
Atom Count: 3,969
Modelled Residue Count: 433
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microbial rhodopsin	A, B	220	marine Actinobacteria clade	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 AA [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] C [auth A] D [auth A] E [auth A] N [auth A] AA [auth B], C [auth A], D [auth A], E [auth A], N [auth A], O [auth A], S [auth A], T [auth A], Y [auth B], Z [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain AA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain V [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain V [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain V [auth A]	GA [auth B], V [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain GA [auth B] Focus chain V [auth A] Interactions & Density Focus chain GA [auth B] Focus chain V [auth A]
LFA Query on LFA Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] 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 P [auth A] SDF format, chain R [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] 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 P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] 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 P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] F [auth A] BA [auth B], CA [auth B], DA [auth B], EA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth A], R [auth A], W [auth B], X [auth B]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain R [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain R [auth A] Focus chain W [auth B] Focus chain X [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain FA [auth B] MOL2 format, chain FA [auth B] mmCIF format, chain FA [auth B]	FA [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain FA [auth B] Interactions & Density Focus chain FA [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Q [auth A] SDF format, chain U [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain U [auth A]	M [auth A], Q [auth A], U [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain Q [auth A] Focus chain U [auth A] Interactions & Density Focus chain M [auth A] Focus chain Q [auth A] Focus chain U [auth A]