9JOU | pdb_00009jou

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

PDB DOI: https://doi.org/10.2210/pdb9JOU/pdb
EM Map EMD-61685: 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: 2.46 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: 156.66 kDa
Atom Count: 9,913
Modeled Residue Count: 1,150
Deposited Residue Count: 1,300
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	260	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
K3I Query on K3I Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain K [auth A] SDF format, chain NA [auth E] SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C]	GA [auth D], K [auth A], NA [auth E], R [auth B], Z [auth C]	Zeaxanthin C₄₀ H₅₆ O₂ JKQXZKUSFCKOGQ-VSRJLPPESA-N		Interactions Focus chain GA [auth D] Focus chain K [auth A] Focus chain NA [auth E] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain K [auth A] Focus chain NA [auth E] Focus chain R [auth B] Focus chain Z [auth C]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain IA [auth E] SDF format, chain N [auth B] SDF format, chain U [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C]	BA [auth D], F [auth A], IA [auth E], N [auth B], U [auth C]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain BA [auth D] Focus chain F [auth A] Focus chain IA [auth E] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain F [auth A] Focus chain IA [auth E] Focus chain N [auth B] Focus chain U [auth C]
R16 (Subject of Investigation/LOI) Query on R16 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	AA [auth D] CA [auth D] DA [auth D] EA [auth D] G [auth A] AA [auth D], CA [auth D], DA [auth D], EA [auth D], G [auth A], H [auth A], JA [auth E], KA [auth E], O [auth B], S [auth C], T [auth C], V [auth C], W [auth C]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain W [auth C]
D12 (Subject of Investigation/LOI) Query on D12 Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth B] SDF format, chain MA [auth E] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	FA [auth D] HA [auth E] I [auth A] J [auth A] L [auth A] FA [auth D], HA [auth E], I [auth A], J [auth A], L [auth A], LA [auth E], M [auth B], MA [auth E], P [auth B], Q [auth B], X [auth C], Y [auth C]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth B] Focus chain MA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth B] Focus chain MA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Y [auth C]