8R0P | pdb_00008r0p

Cryo-EM structure of the microbial rhodopsin CryoR2 at pH 8.0 in detergent

PDB DOI: https://doi.org/10.2210/pdb8R0P/pdb
EM Map EMD-18800: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Subtercola endophyticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-31 Released: 2025-05-14
Deposition Author(s): Kovalev, K., Marin, E., Stetsenko, A., Guskov, A., Lamm, G.H.U.
Funding Organization(s): EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.44 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

CryoRhodopsins: A comprehensive characterization of a group of microbial rhodopsins from cold environments.

Lamm, G.H.U., Marin, E., Alekseev, A., Schellbach, A.V., Stetsenko, A., Haro-Moreno, J.M., Bourenkov, G., Borshchevskiy, V., Asido, M., Agthe, M., Engilberge, S., Rose, S.L., Caramello, N., Royant, A., Schneider, T.R., Bateman, A., Mager, T., Moser, T., Rodriguez-Valera, F., Wachtveitl, J., Guskov, A., Kovalev, K.

(2025) Sci Adv 11: eadv1015-eadv1015

PubMed: 40614199 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adv1015
Primary Citation Related Structures:
8R0K, 8R0L, 8R0M, 8R0N, 8R0O, 8R0P

PubMed Abstract:
Microbial rhodopsins are omnipresent on Earth; however, the vast majority of them remain uncharacterized. Here, we describe a rhodopsin group found in microorganisms from cold environments, such as glaciers, denoted as CryoRhodopsins (CryoRs). A distinguishing feature of the group is the presence of a buried arginine residue close to the cytoplasmic face. Combining single-particle cryo-electron microscopy and x-ray crystallography with rhodopsin activation by light, we demonstrate that the arginine stabilizes an ultraviolet (UV)-absorbing intermediate of an extremely slow CryoRhodopsin photocycle. Together with extensive spectroscopic characterization, our investigations on CryoR1 and CryoR2 proteins reveal mechanisms of photoswitching in the identified group. Our data suggest that CryoRs are sensors for UV irradiation and are also capable of inward proton translocation modulated by UV light.

Organizational Affiliation

Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 186.18 kDa
Atom Count: 11,154
Modeled Residue Count: 1,410
Deposited Residue Count: 1,635
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
microbial rhodopsin CryoR2	A, B, C, D, E	327	Subtercola endophyticus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET (Subject of Investigation/LOI) Query on RET Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain SA [auth E] SDF format, chain M [auth A] SDF format, chain KA [auth D] SDF format, chain CA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain CA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain CA [auth C]	CA [auth C], KA [auth D], M [auth A], SA [auth E], U [auth B]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain CA [auth C] Focus chain KA [auth D] Focus chain M [auth A] Focus chain SA [auth E] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain KA [auth D] Focus chain M [auth A] Focus chain SA [auth E] Focus chain U [auth B]
LFA Query on LFA Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain RA [auth E] SDF format, chain R [auth B] SDF format, chain QA [auth E] SDF format, chain Q [auth B] SDF format, chain PA [auth E] SDF format, chain P [auth B] SDF format, chain OA [auth E] SDF format, chain O [auth B] SDF format, chain NA [auth E] SDF format, chain N [auth B] SDF format, chain MA [auth E] SDF format, chain LA [auth E] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain I [auth A] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain F [auth A] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain MA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth E] mmCIF format, chain N [auth B] mmCIF format, chain MA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] DA [auth D] EA [auth D] F [auth A] AA [auth C], BA [auth C], DA [auth D], EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], L [auth A], LA [auth E], MA [auth E], N [auth B], NA [auth E], O [auth B], OA [auth E], P [auth B], PA [auth E], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], T [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain N [auth B] Focus chain NA [auth E] Focus chain O [auth B] Focus chain OA [auth E] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain N [auth B] Focus chain NA [auth E] Focus chain O [auth B] Focus chain OA [auth E] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]