9IN9

Structure of the viral channelrhodopsin OLPVR1 at low pH obtained by soaking

PDB DOI: https://doi.org/10.2210/pdb9IN9/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Organic Lake phycodnavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-05 Released: 2025-03-12
Deposition Author(s): Bukhdruker, S., Zabelskii, D., Astashkin, R., Gordeliy, V.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free:
0.218 (Depositor), 0.217 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Ion conducting and gating molecular mechanisms of channelrhodopsin revealed by true-atomic resolution structures of open and closed states

Zabelskii, D., Bukhdruker, S., Bukhalovich, S., Tsybrov, F., Lamm, G.H.U., Astashkin, R., Doroginin, D., Matveev, G., Sudarev, V., Kuzmin, A., Zinovev, E., Vlasova, A., Ryzhykau, Y., Ilyinsky, N., Gushchin, I., Bourenkov, G., Alekseev, A., Round, A., Wachtveitl, J., Bamberg, E., Gordeliy, V.

(2025) Nat Struct Mol Biol

Macromolecule Content

Total Structure Weight: 35.82 kDa
Atom Count: 2,985
Modelled Residue Count: 225
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Viral rhodopsin OLPVR1	A	231	Organic Lake phycodnavirus	Mutation(s): 0 Gene Names: 162281038
UniProt
Find proteins for F2Y337 (Organic Lake phycodnavirus) Explore F2Y337 Go to UniProtKB: F2Y337
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F2Y337
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A]	T [auth A], U [auth A], V [auth A], W [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]
97N Query on 97N Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate C₁₉ H₃₆ O₄ KVYUBFKSKZWZSV-ZEVQVBBLSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
LFA Query on LFA Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] D [auth A] E [auth A] F [auth A] G [auth A] AA [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], R [auth A], S [auth A], X [auth A], Y [auth A], Z [auth A]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	A	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.218 (Depositor), 0.217 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.235	α = 90
b = 115.755	β = 90
c = 53.214	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
STARANISO	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-15-CE11-0029-02
Agence Nationale de la Recherche (ANR)	France	ANR-19-CE11-0026
Agence Nationale de la Recherche (ANR)	France	ANR-11-LABX-0015-01