7AKW

Crystal structure of the viral rhodopsins chimera O1O2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.246 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 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
chimera of viral rhodopsins OLPVR1 and OLPVRII
A, B
223Organic Lake phycodnavirusMutation(s): 9 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.246 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.405α = 90
b = 103.396β = 90.32
c = 111.381γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted RETClick 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
  • Version 1.2: 2024-11-06
    Changes: Structure summary