9SOE | pdb_00009soe

Crystal structure of viral channelrhodopsin OLPVR1 in a complex with barium ion bound at the surface

• PDB DOI: https://doi.org/10.2210/pdb9SOE/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Organic Lake phycodnavirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-09-12 Released: 2026-09-23 
• Deposition Author(s): Bukhdruker, S., Zabelskii, D., Gordeliy, V.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.249 (Depositor) 
• R-Value Work: 
  0.207 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

wwPDB Validation

Currently 9SOE does not have a validation slider image.

Literature

Molecular mechanism of calcium inhibition in viral channelrhodopsins.

Zabelskii, D., Bukhdruker, S., Lamm, G.H.U., Bukhalovich, S., Aoyama, M., Sudarev, V., Kuzmin, A., Shibata, M., Kotayama, K., Kandori, H., Wachtveitl, J., Bamberg, E., Gordeliy, V.

(2026) Nat Commun 17

• PubMed: 42749743 
• DOI: https://doi.org/10.1038/s41467-026-77716-5
• Primary Citation Related Structures: 
  9SOD, 9SOE, 9SOF, 9SOG


• PubMed Abstract: 
  

  Viral channelrhodopsins (VCR1s) are giant-virus-encoded light-gated channels permeable to monovalent and divalent cations, including Na ⁺ and Ca ²⁺ ions, and inhibited by millimolar Ca ²⁺ concentrations. Here, we combine X-ray crystallography, time-resolved UV-vis spectroscopy, and ATR-FTIR spectroscopy to investigate molecular mechanisms of ion permeation and Ca ²⁺ -dependent inhibition in OLPVR1. An atomic resolution structure of OLPVR1 obtained in the presence of 10 mM CaCl ₂ and 900 mM NaCl reveals a transient intracellular Ca ²⁺ binding site near T87 and T88, close to the retinal cofactor. Upon photoactivation, this Ca ²⁺ ion prevents a key rearrangement of the intracellular gate required for ion translocation, namely the flip of E44, thereby disrupting ion conduction. Instead, illumination leads to the accumulation of Na ⁺ ions between E44, S208 and the carbonyl oxygen of retinal-binding residue K204. Our findings reveal the molecular basis of Ca ²⁺ -dependent inhibition in VCR1s and provide a foundation for engineering enhanced tools for calcium optogenetics.

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Organizational Affiliation: 
• European X-ray Free Electron Laser GmbH, Schenefeld, Germany. [e-mail].
European Molecular Biology Laboratory, Hamburg, Germany. [e-mail].
Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.
WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, Japan.
Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan.
OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.
Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.41 kDa 
• Atom Count: 2,233 
• Modeled Residue Count: 223 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rhodopsin	A	231	Organic Lake phycodnavirus	Mutation(s): 0  Gene Names: 162281038

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	U [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
97N	R [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate C19 H36 O4 KVYUBFKSKZWZSV-ZEVQVBBLSA-N
RET	Y [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
LFA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth A], V [auth A]	EICOSANE C20 H42 CBFCDTFDPHXCNY-UHFFFAOYSA-N
BA( Subject of Investigation/LOI)	X [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
GOL	T [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	W [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.249 (Depositor) 
• R-Value Work:  0.207 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.219	α = 90
b = 115.034	β = 90
c = 53.294	γ = 90

Software Package:

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

Structure Validation

Currently 9SOE does not have a validation slider image.

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-23 
Deposition Author(s): Bukhdruker, S., Zabelskii, D., Gordeliy, V.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-19-CE11-0026

Revision History  

• Version 1.0: 2026-09-23
  Type: Initial release
  
• Version 1.1: 2026-09-30
  Changes: Database references