PDBsum entry 1k4r

Virus

PDB id: 1k4r

Contents

Protein chains

395 a.a. *

* Residue conservation analysis

PDB id:

1k4r

Name:

Virus

Title:

Structure of dengue virus

Structure:

Major envelope protein e. Chain: a, b, c. Fragment: unp residues 284-678

Source:

Chimeric tick-borne encephalitis virus/dengue virus 4. Organism_taxid: 638787

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

Key ref:

R.J.Kuhn et al. (2002). Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell, 108, 717-725. PubMed id: 11893341 DOI: 10.1016/S0092-8674(02)00660-8

Date:

08-Oct-01 Release date: 13-Mar-02

Protein chains

C3V005  (C3V005_9FLAV) -  Genome polyprotein from Chimeric Tick-borne encephalitis virus/Dengue virus 4

Seq: 3392 a.a.

Struc: 395 a.a.*

* PDB and UniProt seqs differ at 12 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.3.4.21.91 - flavivirin.
• Reaction: Selective hydrolysis of Xaa-Xaa-|-Xbb bonds in which each of the Xaa can be either Arg or Lys and Xbb can be either Ser or Ala.
• Enzyme class 2: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 3: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0092-8674(02)00660-8

Cell 108:717-725 (2002)

PubMed id: 11893341

Structure of dengue virus: implications for flavivirus organization, maturation, and fusion.

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.

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.

Selected figure(s)

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.

The above figures are reprinted by permission from Cell Press: Cell (2002, 108, 717-725) copyright 2002.

Figures were selected by an automated process.