Journal: J Mol Biol / Year: 2011 Title: Molecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus. Authors: Jinghua Tang / Joyce Jose / Paul Chipman / Wei Zhang / Richard J Kuhn / Timothy S Baker / Abstract: A three-dimensional reconstruction of Sindbis virus at 7.0 Å resolution presented here provides a detailed view of the virion structure and includes structural evidence for key interactions that ...A three-dimensional reconstruction of Sindbis virus at 7.0 Å resolution presented here provides a detailed view of the virion structure and includes structural evidence for key interactions that occur between the capsid protein (CP) and transmembrane (TM) glycoproteins E1 and E2. Based on crystal structures of component proteins and homology modeling, we constructed a nearly complete, pseudo-atomic model of the virus. Notably, this includes identification of the 33-residue cytoplasmic domain of E2 (cdE2), which follows a path from the E2 TM helix to the CP where it enters and exits the CP hydrophobic pocket and then folds back to contact the viral membrane. Modeling analysis identified three major contact regions between cdE2 and CP, and the roles of specific residues were probed by molecular genetics. This identified R393 and E395 of cdE2 and Y162 and K252 of CP as critical for virus assembly. The N-termini of the CPs form a contiguous network that interconnects 12 pentameric and 30 hexameric CP capsomers. A single glycoprotein spike cross-links three neighboring CP capsomers as might occur during initiation of virus budding.
History
Deposition
Nov 23, 2010
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Header (metadata) release
May 5, 2011
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Map release
Oct 6, 2011
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Update
May 22, 2012
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Current status
May 22, 2012
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shell
Shell ID: 1 / Diameter: 700 Å / T number (triangulation number): 4
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Vitrification
Cryogen name: ETHANE / Instrument: OTHER
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Electron microscopy
Microscope
FEI/PHILIPS CM300FEG/T
Date
Dec 12, 2001
Image recording
Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 73 / Od range: 1 / Bits/pixel: 8
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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