PDBsum entry 1k4r

Virus

PDB id

1k4r

Contents

			Protein chains

					395 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of dengue virus: implications for flavivirus organization, Maturation, And fusion.

Authors

R.J.Kuhn, W.Zhang, M.G.Rossmann, S.V.Pletnev, J.Corver, E.Lenches, C.T.Jones, S.Mukhopadhyay, P.R.Chipman, E.G.Strauss, T.S.Baker, J.H.Strauss.

Ref.

Cell, 2002, 108, 717-725. [DOI no: 10.1016/S0092-8674(02)00660-8]

PubMed id

11893341

Abstract

The first structure of a flavivirus has been determined by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron density map. The virus core, within a lipid bilayer, has a less-ordered structure than the external, icosahedral scaffold of 90 glycoprotein E dimers. The three E monomers per icosahedral asymmetric unit do not have quasiequivalent symmetric environments. Difference maps indicate the location of the small membrane protein M relative to the overlaying scaffold of E dimers. The structure suggests that flaviviruses, and by analogy also alphaviruses, employ a fusion mechanism in which the distal beta barrels of domain II of the glycoprotein E are inserted into the cellular membrane.



	Figure 1. Figure 1. The CryoEM Density(A) Surface-shaded representation of dengue-2 cryoEM reconstruction at 24 Å resolution, showing the outline of one icosahedral asymmetric unit and the definition of the coordinate system. Scale bar represents 100 Å.(B) Central crosssection showing the cryo-EM density with a plot of the maximum (blue) and averaged (purple) density. Arrows indicate the position of the 5-fold and 3-fold axes. Shown also are radial density sections at the defined radii, r1, r2, r3, and r4. Higher density representing protein is shown in dark shading. Scale bar represents 175 Å.(C) Ribbon drawing of the E dimer situated on an icosahedral 2-fold axis, showing the largest uninterpreted electron density peak outside the lipid bilayer, probably representing the M protein (light blue), located close to the hole between the E dimers. The white arrow indicates the position of the dimer holes. The outer leaflet of the lipid bilayer is shown in green. The domains I, II, and III of an E monomer are shown in red, yellow, and blue, respectively. The fusion peptides are in green.(D) Ribbon drawing showing the position and orientation of the E dimer associated with an icosahedral 2-fold axis. Shown in white is the outline of one icosahedral asymmetric unit. The domains of E are colored as in (C). The portion of the membrane protein M below the dimer is indicated.		Figure 2. Figure 2. CryoEM Density of the Nucleocapsid Shell and the RNA(A) Stereo diagram of the region corresponding to the yellow nucleocapsid shell in Figure 1, between 105 and 135 Å radii.(B) Stereo diagram of density corresponding to the RNA region of the core (red in Figure 1), inside a radius of 105 Å. Only one hemisphere is shown. Scale bars represent 100 Å.