6ZQI

Cryo-EM structure of Spondweni virus prME

Summary for 6ZQI

• Entry DOI: 10.2210/pdb6zqi/pdb
• EMDB information: 11364
• Descriptor: Genome polyprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
• Functional Keywords: flavivirus, virus
• Biological source: Spondweni virus; More
• Total number of polymer chains: 3
• Total formula weight: 93200.92

Authors

Renner, M.,Dejnirattisai, W.,Carrique, L.,Serna Martin, I.,Karia, D.,Ilca, S.L.,Ho, S.F.,Kotecha, A.,Keown, J.R.,Mongkolsapaya, J.,Screaton, G.R.,Grimes, J.M. (deposition date: 2020-07-09, release date: 2021-01-20, Last modification date: 2021-08-04)

Primary citation

Renner, M.,Dejnirattisai, W.,Carrique, L.,Martin, I.S.,Karia, D.,Ilca, S.L.,Ho, S.F.,Kotecha, A.,Keown, J.R.,Mongkolsapaya, J.,Screaton, G.R.,Grimes, J.M.
Flavivirus maturation leads to the formation of an occupied lipid pocket in the surface glycoproteins.
Nat Commun, 12:1238-1238, 2021

PubMed Abstract: Flaviviruses such as Dengue (DENV) or Zika virus (ZIKV) assemble into an immature form within the endoplasmatic reticulum (ER), and are then processed by furin protease in the trans-Golgi. To better grasp maturation, we carry out cryo-EM reconstructions of immature Spondweni virus (SPOV), a human flavivirus of the same serogroup as ZIKV. By employing asymmetric localised reconstruction we push the resolution to 3.8 Å, enabling us to refine an atomic model which includes the crucial furin protease recognition site and a conserved Histidine pH-sensor. For direct comparison, we also solve structures of the mature forms of SPONV and DENV to 2.6 Å and 3.1 Å, respectively. We identify an ordered lipid that is present in only the mature forms of ZIKV, SPOV, and DENV and can bind as a consequence of rearranging amphipathic stem-helices of E during maturation. We propose a structural role for the pocket and suggest it stabilizes mature E.

PubMed: 33623019
DOI: 10.1038/s41467-021-21505-9

Experimental method

ELECTRON MICROSCOPY (3.8 Å)