9JOV | pdb_00009jov

Cryo-EM structure of the myxol-bound light-driven proton pumping rhodopsin, NM-R1

PDB DOI: https://doi.org/10.2210/pdb9JOV/pdb
EM Map EMD-61686: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Nonlabens marinus S1-08
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-25 Released: 2025-07-30
Deposition Author(s): Hosaka, T., Shirouzu, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.27 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

Intracellular carotenoids enhance the pump activation of microbial rhodopsin in two ways: The light-harvesting antenna and the photocycle acceleration

Fujiwara, T., Hosaka, T., Hasegawa-Takano, M., Nishimura, Y., Tominaga, K., Mori, K., Nishino, S., Kawasaki, Y., Takahashi, Y., Uchikubo-Kamo, T., Hanada, K., Takaichi, S., Inoue, K., Shirouzu, M., Yoshizawa, S.

To be published.

Macromolecule Content

Total Structure Weight: 154.46 kDa
Atom Count: 10,041
Modeled Residue Count: 1,150
Deposited Residue Count: 1,270
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteorhodopsin	A, B, C, D, E	254	Nonlabens marinus S1-08	Mutation(s): 0 Gene Names: NMS_0162
UniProt
Find proteins for W8VZ92 (Nonlabens marinus S1-08) Explore W8VZ92 Go to UniProtKB: W8VZ92
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W8VZ92
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L4O Query on A1L4O Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain JA [auth D] SDF format, chain L [auth A] SDF format, chain RA [auth E] SDF format, chain T [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain T [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain T [auth B]	BA [auth C], JA [auth D], L [auth A], RA [auth E], T [auth B]	(3~{S},4~{Z},6~{E},8~{Z},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E})-2,6,10,14,19,23-hexamethyl-25-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]pentacosa-4,6,8,10,12,14,16,18,20,22,24-undecaene-2,3-diol C₄₀ H₅₆ O₃ JJPMVSRTRMLHST-CNFSYYPWSA-N		Interactions Focus chain BA [auth C] Focus chain JA [auth D] Focus chain L [auth A] Focus chain RA [auth E] Focus chain T [auth B] Interactions & Density Focus chain BA [auth C] Focus chain JA [auth D] Focus chain L [auth A] Focus chain RA [auth E] Focus chain T [auth B]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain NA [auth E] SDF format, chain P [auth B] SDF format, chain X [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain NA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain NA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C]	F [auth A], FA [auth D], NA [auth E], P [auth B], X [auth C]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain F [auth A] Focus chain FA [auth D] Focus chain NA [auth E] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain F [auth A] Focus chain FA [auth D] Focus chain NA [auth E] Focus chain P [auth B] Focus chain X [auth C]
R16 (Subject of Investigation/LOI) Query on R16 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth E] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain SA [auth E] SDF format, chain U [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	CA [auth C] DA [auth D] G [auth A] GA [auth D] H [auth A] CA [auth C], DA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], KA [auth D], LA [auth E], M [auth A], N [auth A], OA [auth E], Q [auth B], R [auth B], SA [auth E], U [auth B], V [auth C], Y [auth C], Z [auth C]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [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 KA [auth D] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth C] Focus chain DA [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 KA [auth D] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
D12 (Subject of Investigation/LOI) Query on D12 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth D] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain MA [auth E] SDF format, chain O [auth A] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain S [auth B] SDF format, chain W [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C]	AA [auth C] EA [auth D] IA [auth D] J [auth A] K [auth A] AA [auth C], EA [auth D], IA [auth D], J [auth A], K [auth A], MA [auth E], O [auth A], PA [auth E], QA [auth E], S [auth B], W [auth C]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth E] Focus chain O [auth A] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain S [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth E] Focus chain O [auth A] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain S [auth B] Focus chain W [auth C]