PDBsum entry 1d1d

Viral protein

PDB id: 1d1d

Contents

Protein chain

220 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Solution structure and dynamics of the rous sarcoma virus capsid protein and comparison with capsid proteins of other retroviruses.

Authors

R.Campos-Olivas, J.L.Newman, M.F.Summers.

Ref.

J Mol Biol, 2000, 296, 633-649. [DOI no: 10.1006/jmbi.1999.3475]

PubMed id

10669613

Abstract

The solution structure and dynamics of the recombinant 240 amino acid residue capsid protein from the Rous sarcoma virus has been determined by NMR methods. The structure was determined using 2200 distance restraints and 330 torsion angle restraints, and the dynamics analysis was based on (15)N relaxation parameters (R(1), R(2), and (1)H-(15)N NOE) measured for 153 backbone amide groups. The monomeric protein consists of independently folded N- and C-terminal domains that comprise residues Leu14-Leu146 and Ala150-Gln226, respectively. The domains exhibit different rotational correlation times (16.6(+/-0.1) ns and 12.6(+/-0.1) ns, respectively), are connected by a flexible linker (Ala147-Pro149), and do not give rise to inter-domain NOE values, indicating that they are dynamically independent. Despite limited sequence similarity, the structure of the Rous sarcoma virus capsid protein is similar to the structures determined recently for the capsid proteins of retroviruses belonging to the lentivirus and human T-cell leukemia virus/bovine leukemia virus genera. Structural differences that exist in the C-terminal domain of Rous sarcoma virus capsid relative to the other capsid proteins appear to be related to the occurrence of conserved cysteine residues. Whereas most genera of retroviruses contain a pair of conserved and essential cysteine residues in the C-terminal domain that appear to function by forming an intramolecular disulfide bond during assembly, the Rous sarcoma virus capsid protein does not. Instead, the Rous sarcoma virus capsid protein contains a single cysteine residue that appears to be conserved among the avian C-type retroviruses and is positioned in a manner that might allow the formation of an intermolecular disulfide bond during capsid assembly.

Figure 4.
Figure 4. Ribbon representations of two views (which differ by a 90 ° rotation about the vertical axis) of a representative CA[RSV] structure.

Figure 10.
Figure 10. Model of a potential RSV capsid CTD dimer, generated by superposition of two RSV CA CTDs onto the dimeric HIV-1 CA CTD (not shown). This illustrates that Cys192 is poised to potentially form an intermolecular disulfide bond if this domain forms a dimer in a manner similar to that observed for both the HIV-1 and EIAV capsid proteins.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 296, 633-649) copyright 2000.