7AKX

Crystal structure of the viral rhodopsin OLPVR1 in P1 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 OLPVR1
A, B
231Organic 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
J [auth A],
X [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
FA [auth B],
GA [auth B],
H [auth A],
HA [auth B],
I [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 B],
S [auth B],
T [auth B],
V [auth B],
W [auth B],
Z [auth B]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
U [auth B],
Y [auth B]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LYR
Query on LYR
A, B
L-PEPTIDE LINKINGC26 H42 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.177α = 113.9
b = 56.968β = 90.01
c = 62.34γ = 91.49
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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