9JTQ | pdb_00009jtq

Crystal structure of the light-driven proton pump heimdallarchaeial rhodopsin HeimdallR1

• PDB DOI: https://doi.org/10.2210/pdb9JTQ/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Candidatus Heimdallarchaeota archaeon
• Expression System: Expression vector pET-mod
• Mutation(s): No 


• Deposited: 2024-10-06 Released: 2025-04-02 
• Deposition Author(s): Matsuzaki, Y., Tzlil, G., Del Carmen Marin, M., Shihoya, W., Beja, O., Nureki, O.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea.

Tzlil, G., Marin, M.D.C., Matsuzaki, Y., Nag, P., Itakura, S., Mizuno, Y., Murakoshi, S., Tanaka, T., Larom, S., Konno, M., Abe-Yoshizumi, R., Molina-Marquez, A., Barcenas-Perez, D., Cheel, J., Koblizek, M., Leon, R., Katayama, K., Kandori, H., Schapiro, I., Shihoya, W., Nureki, O., Inoue, K., Rozenberg, A., Chazan, A., Beja, O.

(2025) Nat Microbiol 10: 1484-1500

• PubMed: 40442502 
• DOI: https://doi.org/10.1038/s41564-025-02016-5
• Primary Citation of Related Structures:  
  9JTQ


• PubMed Abstract: 
  

  Aquatic bacterial rhodopsin proton pumps harvest light energy for photoheterotrophic growth and are known to contain hydroxylated carotenoids that expand the wavelengths of light utilized, but these have not been characterized in marine archaea. Here, by combining a marine chromophore extract with purified archaeal rhodopsins identified in marine metagenomes, we show light energy transfer from diverse hydroxylated carotenoids to heimdallarchaeial rhodopsins (HeimdallRs) from uncultured marine planktonic members of 'Candidatus Kariarchaeaceae' ('Candidatus Asgardarchaeota'). These light-harvesting antennas absorb in the blue-light range and transfer energy to the green-light-absorbing retinal chromophore within HeimdallRs, enabling the use of light that is otherwise unavailable to the rhodopsin. Furthermore, we show elevated proton pumping by the antennas in HeimdallRs under white-light illumination, which better simulates the light conditions encountered by these archaea in their natural habitats. Our results indicate that light-harvesting antennas in microbial rhodopsins exist in families beyond xanthorhodopsins and proteorhodopsins and are present in both marine bacteria and archaea.

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Organizational Affiliation: 
• Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
Physical and Analytical Chemistry Department, University of Jaén, Jaén, Spain.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan.
The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.
Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, Huelva, Spain.
Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Třeboň, Czech Republic.
Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan.
Department of Physics, Technische Universität, Dortmund, Germany.
Research Center Chemical Sciences and Sustainability, University Alliance Ruhr, Bochum, Germany.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. [e-mail].
The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan. [e-mail].
Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel. [e-mail].
Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel. [e-mail].
Institute of Environmental Engineering, ETH, Zurich, Switzerland. [e-mail].
Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel. [e-mail].
The Nancy and Stephen Grand Technion Energy Program (GTEP), Technion-Israel Institute of Technology, Haifa, Israel. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.66 kDa 
• Atom Count: 2,223 
• Modeled Residue Count: 248 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A	254	Candidatus Heimdallarchaeota archaeon	Mutation(s): 0  Gene Names: CME83_04245

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	C [auth A], D [auth A], F [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET (Subject of Investigation/LOI)	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
NO3	E [auth A], G [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.59	α = 90
b = 60.37	β = 90
c = 86.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Matsuzaki, Y., Tzlil, G., Del Carmen Marin, M., Shihoya, W., Beja, O., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21H05037

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-12-03
  Changes: Database references