5FOJ

Cryo electron microscopy structure of Grapevine Fanleaf Virus complex with Nanobody

Summary for 5FOJ

• Entry DOI: 10.2210/pdb5foj/pdb
• EMDB information: 3246
• Descriptor: Nanobody, RNA2 polyprotein (2 entities in total)
• Functional Keywords: virus, nanobody, complex
• Biological source: Camelus dromedarius (Camel); More
• Total number of polymer chains: 2
• Total formula weight: 70889.48

Authors

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. (deposition date: 2015-11-22, release date: 2016-01-20, Last modification date: 2021-08-11)

Primary citation

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.
Structural basis of nanobody recognition of grapevine fanleaf virus and of virus resistance loss.
Proc.Natl.Acad.Sci.USA, 2020

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.

PubMed: 32371486
DOI: 10.1073/pnas.1913681117

Experimental method

ELECTRON MICROSCOPY (2.8 Å)