7AKY

Crystal structure of the viral rhodopsin OLPVR1 in P21212 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.143 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.145 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 97NClick on this verticalbar to view detailsBest fitted LFAClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Viral rhodopsins 1 are an unique family of light-gated cation channels.

Zabelskii, D.Alekseev, A.Kovalev, K.Rankovic, V.Balandin, T.Soloviov, D.Bratanov, D.Savelyeva, E.Podolyak, E.Volkov, D.Vaganova, S.Astashkin, R.Chizhov, I.Yutin, N.Rulev, M.Popov, A.Eria-Oliveira, A.S.Rokitskaya, T.Mager, T.Antonenko, Y.Rosselli, R.Armeev, G.Shaitan, K.Vivaudou, M.Buldt, G.Rogachev, A.Rodriguez-Valera, F.Kirpichnikov, M.Moser, T.Offenhausser, A.Willbold, D.Koonin, E.Bamberg, E.Gordeliy, V.

(2020) Nat Commun 11: 5707-5707

  • DOI: https://doi.org/10.1038/s41467-020-19457-7
  • Primary Citation of Related Structures:  
    7AKW, 7AKX, 7AKY

  • PubMed Abstract: 

    Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that infect phytoplankton organisms and regulate the phytoplankton dynamics encompass genes of rhodopsins of two distinct families. Here, we present a functional and structural characterization of two proteins of viral rhodopsin group 1, OLPVR1 and VirChR1. Functional analysis of VirChR1 shows that it is a highly selective, Na + /K + -conducting channel and, in contrast to known cation channelrhodopsins, it is impermeable to Ca 2+ ions. We show that, upon illumination, VirChR1 is able to drive neural firing. The 1.4 Å resolution structure of OLPVR1 reveals remarkable differences from the known channelrhodopsins and a unique ion-conducting pathway. Thus, viral rhodopsins 1 represent a unique, large group of light-gated channels (viral channelrhodopsins, VirChR1s). In nature, VirChR1s likely mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, might play a major role in global phytoplankton dynamics. Moreover, VirChR1s have unique potential for optogenetics as they lack possibly noxious Ca 2+ permeability.


  • Organizational Affiliation

    Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
viral rhodopsin OLPVR1231Organic Lake phycodnavirusMutation(s): 0 
Gene Names: 162281038
Membrane Entity: Yes 
UniProt
Find proteins for F2Y337 (Organic Lake phycodnavirus)
Explore F2Y337 
Go to UniProtKB:  F2Y337
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Y337
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
97N
Query on 97N

Download Ideal Coordinates CCD File 
W [auth A](2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate
C19 H36 O4
KVYUBFKSKZWZSV-ZEVQVBBLSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LYR
Query on LYR
A
L-PEPTIDE LINKINGC26 H42 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.143 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.145 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.525α = 90
b = 115.796β = 90
c = 53.529γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 97NClick on this verticalbar to view detailsBest fitted LFAClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-19-CE11-0026
Russian Foundation for Basic ResearchRussian Federation21-54-12020
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR-10-INBS-05-02

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description