5FOJ

Cryo electron microscopy structure of Grapevine Fanleaf Virus complex with Nanobody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Structural basis of nanobody recognition of grapevine fanleaf virus and of virus resistance loss.

Orlov, I.Hemmer, C.Ackerer, L.Lorber, B.Ghannam, A.Poignavent, V.Hleibieh, K.Sauter, C.Schmitt-Keichinger, C.Belval, L.Hily, J.M.Marmonier, A.Komar, V.Gersch, S.Schellenberger, P.Bron, P.Vigne, E.Muyldermans, S.Lemaire, O.Demangeat, G.Ritzenthaler, C.Klaholz, B.P.

(2020) Proc Natl Acad Sci U S A 

  • DOI: 10.1073/pnas.1913681117
  • Primary Citation of Related Structures:  
    5FOJ

  • PubMed Abstract: 
  • Grapevine fanleaf virus (GFLV) is a picorna-like plant virus transmitted by nematodes that affects vineyards worldwide. Nanobody (Nb)-mediated resistance against GFLV has been created recently, and shown to be highly effective in plants, including grapevine, but the underlying mechanism is unknown ...

    Grapevine fanleaf virus (GFLV) is a picorna-like plant virus transmitted by nematodes that affects vineyards worldwide. Nanobody (Nb)-mediated resistance against GFLV has been created recently, and shown to be highly effective in plants, including grapevine, but the underlying mechanism is unknown. Here we present the high-resolution cryo electron microscopy structure of the GFLV-Nb23 complex, which provides the basis for molecular recognition by the Nb. The structure reveals a composite binding site bridging over three domains of one capsid protein (CP) monomer. The structure provides a precise mapping of the Nb23 epitope on the GFLV capsid in which the antigen loop is accommodated through an induced-fit mechanism. Moreover, we uncover and characterize several resistance-breaking GFLV isolates with amino acids mapping within this epitope, including C-terminal extensions of the CP, which would sterically interfere with Nb binding. Escape variants with such extended CP fail to be transmitted by nematodes linking Nb-mediated resistance to vector transmission. Together, these data provide insights into the molecular mechanism of Nb23-mediated recognition of GFLV and of virus resistance loss.


    Organizational Affiliation

    Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NanobodyA137Camelus dromedariusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA2 polyproteinB504Grapevine fanleaf virusMutation(s): 0 
UniProt
Find proteins for P18474 (Grapevine fanleaf virus)
Explore P18474 
Go to UniProtKB:  P18474
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research Agency--

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-04-13
    Changes: Source and taxonomy
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 2.0: 2020-05-13
    Type: Coordinate replacement
    Reason: Polymer geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Data processing, Database references, Derived calculations, Experimental preparation, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2020-05-20
    Changes: Database references
  • Version 3.0: 2021-08-11
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description