PDBsum entry 1ld4

Virus

PDB id: 1ld4

Contents

Protein chains

151 a.a. *

(+ 2 more) 28 a.a.* *

369 a.a. *

Ligands

UNX ×32

* Residue conservation analysis

* C-alpha coords only

References listed in PDB file

Key reference

• Title: Placement of the structural proteins in sindbis virus.
• Authors: W.Zhang, S.Mukhopadhyay, S.V.Pletnev, T.S.Baker, R.J.Kuhn, M.G.Rossmann.
• Ref.: J Virol, 2002, 76, 11645-11658.
• PubMed id: 12388725

Abstract

The structure of the lipid-enveloped Sindbis virus has been determined by fitting atomic resolution crystallographic structures of component proteins into an 11-A resolution cryoelectron microscopy map. The virus has T=4 quasisymmetry elements that are accurately maintained between the external glycoproteins, the transmembrane helical region, and the internal nucleocapsid core. The crystal structure of the E1 glycoprotein was fitted into the cryoelectron microscopy density, in part by using the known carbohydrate positions as restraints. A difference map showed that the E2 glycoprotein was shaped similarly to E1, suggesting a possible common evolutionary origin for these two glycoproteins. The structure shows that the E2 glycoprotein would have to move away from the center of the trimeric spike in order to expose enough viral membrane surface to permit fusion with the cellular membrane during the initial stages of host infection. The well-resolved E1-E2 transmembrane regions form alpha-helical coiled coils that were consistent with T=4 symmetry. The known structure of the capsid protein was fitted into the density corresponding to the nucleocapsid, revising the structure published earlier.