Biological Assembly 1  

 3D View: Structure

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 120-mer - A60B60 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.89 kDa 
• Atom Count: 4928 
• Modelled Residue Count: 634 
• Deposited Residue Count: 641 
• Unique protein chains: 2

5FOJ

Cryo electron microscopy structure of Grapevine Fanleaf Virus complex with Nanobody

• DOI: 10.2210/pdb5FOJ/pdb
• EMDataResource: EMD-3246

• Classification: VIRUS
• Organism(s): Camelus dromedarius, Grapevine fanleaf virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-22 Released: 2016-01-20 
• Deposition Author(s): 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.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

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

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 

• PubMed: 32371486 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	A	137	Camelus dromedarius	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA2 polyprotein	B	504	Grapevine fanleaf virus	Mutation(s): 0
UniProt
Find proteins for P18474 (Grapevine fanleaf virus) Explore P18474  Go to UniProtKB:  P18474

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-22 
• Released Date: 2016-01-20 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
French National Research Agency		--

Revision History  

• 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