PDBsum entry 1vcq

Viral protein

PDB id: 1vcq

Contents

Protein chains

149 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Structure of semliki forest virus core protein.
• Authors: H.K.Choi, G.Lu, S.Lee, G.Wengler, M.G.Rossmann.
• Ref.: Proteins, 1997, 27, 345-359.
• PubMed id: 9094737

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 92%.

Abstract

Alphaviruses are enveloped, insect-borne viruses, which contains a positive-sense RNA genome. The protein capsid is surrounded by a lipid membrane, which is penetrated by glycoprotein spikes. The structure of the Sindbis virus (SINV) (the type virus) core protein (SCP) was previously determined and found to have a chymotrypsin-like structure. SCP is a serine proteinase which cleaves itself from a polyprotein. Semliki Forest virus (SFV) is among the most distantly related alphaviruses to SINV. Similar to SCP, autocatalysis is inhibited in SFCP after cleavage of the polyprotein by leaving the carboxy-terminal tryptophan in the specificity pocket. The structures of two different crystal forms (I and II) of SFV core protein (SFCP) have been determined to 3.0 A and 3.3 A resolution, respectively. The SFCP monomer backbone structure is very similar to that of SCP. The dimeric association between monomers, A and B, found in two different crystal forms of SCP is also present in both crystal forms of SFCP. However, a third monomer, C, occurs in SFCP crystal form I. While monomers A and B make a tail-to-tail dimer contact, monomers B and C make a head-to-head dimer contact. A hydrophobic pocket on the surface of the capsid protein, the proposed site of binding of the E2 glycoprotein, has large conformational differences with respect to SCP and, in contrast to SCP, is found devoid of bound peptide. In particular, Tyr184 is pointing out of the hydrophobic pocket in SFCP, whereas the equivalent tyrosine in SCP is pointing into the pocket. The conformation of Tyr184, found in SFCP, is consistent with its availability for iodination, as observed in the homologous SINV cores. This suggests, by comparison with SCP, that E2 binding to cores causes major conformational changes, including the burial of Tyr184, which would stabilize the intact virus on budding from an infected cell. The head-to-tail contacts found in the pentameric and hexameric associations within the virion utilize in the same monomer surface regions as found in the crystalline dimer interfaces.

Secondary reference #1

• Title: Refined structure of sindbis virus core protein and comparison with other chymotrypsin-Like serine proteinase structures.
• Authors: L.Tong, G.Wengler, M.G.Rossmann.
• Ref.: J Mol Biol, 1993, 230, 228-247.
• PubMed id: 8450538

Secondary reference #2

• Title: Structure of sindbis virus core protein reveals a chymotrypsin-Like serine proteinase and the organization of the virion.
• Authors: H.K.Choi, L.Tong, W.Minor, P.Dumas, U.Boege, M.G.Rossmann, G.Wengler.
• Ref.: Nature, 1991, 354, 37-43.
• PubMed id: 1944569