5UK1

CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 3

Summary for 5UK1

• Entry DOI: 10.2210/pdb5uk1/pdb
• Related: 5UJZ 5UK0 5UK2
• EMDB information: 8561 8562 8563 8564
• Descriptor: Hemagglutinin HA1, Hemagglutinin HA2, scFv, ... (6 entities in total)
• Functional Keywords: viral glycoprotein, hemagglutinin, antibody fragment, viral protein-immune system complex, viral protein/immune system
• Biological source: Influenza A virus (A/Solomon Islands/3/2006(H1N1)); More
• Total number of polymer chains: 9
• Total formula weight: 257498.88

Authors

Liu, Y.,Pan, J.,Caradonna, T.,Jenni, S.,Raymond, D.D.,Schmidt, A.G.,Harrison, S.C.,Grigorieff, N. (deposition date: 2017-01-19, release date: 2017-05-31, Last modification date: 2024-10-30)

Primary citation

Liu, Y.,Pan, J.,Jenni, S.,Raymond, D.D.,Caradonna, T.,Do, K.T.,Schmidt, A.G.,Harrison, S.C.,Grigorieff, N.
CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface.
J. Mol. Biol., 429:1829-1839, 2017

PubMed Abstract: Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes.Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain variable-domain fragment complexes, by studying a complex we failed to crystallize in pursuing an extended project on the human immune response to influenza vaccines.The result shows that a combination of cryoEM and molecular modeling can yield details of the antigen-antibody interface, although small variation in the twist of the rod-likeHA trimer limited the overall resolution to about 4.5Å.Comparison of principal 3D classes suggests ways to modify the HA trimer to overcome this limitation. A closely related antibody from the same donor did yield crystals when bound with the same HA, giving us an independent validation of the cryoEM results.The two structures also augment our understanding of receptor-binding site recognition by antibodies that neutralize a wide range of influenza-virus variants.

PubMed: 28506635
DOI: 10.1016/j.jmb.2017.05.011

Experimental method

ELECTRON MICROSCOPY (4.8 Å)