PDBsum entry 1vcp

Viral protein

PDB id: 1vcp

Contents

Protein chains

149 a.a. *

Metals

_HG ×3

* Residue conservation analysis

PDB id:

1vcp

Name:

Viral protein

Title:

Semliki forest virus capsid protein (crystal form i)

Structure:

Semliki forest virus capsid protein. Chain: a, b, c. Engineered: yes. Other_details: crystal form 1

Source:

Semliki forest virus. Organism_taxid: 11033. Organ: kidney. Expressed in: cricetinae gen. Sp.. Expression_system_taxid: 36483

Resolution:

3.00Å R-factor: 0.157

Authors:

G.Lu,H.-K.Choi,M.G.Rossmann

Key ref:

H.K.Choi et al. (1997). Structure of Semliki Forest virus core protein. Proteins, 27, 345-359. PubMed id: 9094737

Date:

04-Mar-96 Release date: 07-Dec-96

Protein chains

P03315  (POLS_SFV) -  Structural polyprotein from Semliki forest virus

Seq: 1253 a.a.

Struc: 149 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.90 - togavirin.
• Reaction: Autocatalytic release of the core protein from the N-terminus of the togavirus structural protein by hydrolysis of a Trp-|-Ser bond.

Proteins 27:345-359 (1997)

PubMed id: 9094737

Structure of Semliki Forest virus core protein.

H.K.Choi, G.Lu, S.Lee, G.Wengler, M.G.Rossmann.

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.