1WYK
SINDBIS VIRUS CAPSID PROTEIN (114-264)
Summary for 1WYK
| Entry DOI | 10.2210/pdb1wyk/pdb |
| Descriptor | SINDBIS VIRUS CAPSID PROTEIN, FORMYL GROUP, 1,4-DIETHYLENE DIOXIDE, ... (4 entities in total) |
| Functional Keywords | coat protein, sindbis, virus, proteinase, alphavirus, capsid, dioxane, viral protein, hydrolase |
| Biological source | Sindbis virus |
| Cellular location | Capsid protein: Virion (By similarity). p62: Virion membrane; Single-pass type I membrane protein (By similarity). E2 envelope glycoprotein: Virion membrane; Single-pass type I membrane protein (By similarity). E1 envelope glycoprotein: Virion membrane; Single-pass type I membrane protein (By similarity). 6K protein: Host cell membrane; Multi-pass membrane protein (By similarity): P27285 |
| Total number of polymer chains | 4 |
| Total formula weight | 67267.94 |
| Authors | Lee, S.,Kuhn, R.J.,Rossmann, M.G. (deposition date: 1998-01-12, release date: 1998-04-29, Last modification date: 2024-04-03) |
| Primary citation | Lee, S.,Kuhn, R.J.,Rossmann, M.G. Probing the potential glycoprotein binding site of sindbis virus capsid protein with dioxane and model building. Proteins, 33:311-317, 1998 Cited by PubMed Abstract: Alphavirus budding from the plasma membrane is initiated by the specific interaction of the nucleocapsid with the cytoplasmic domain of the glycoprotein E2. It was proposed (Lee et al., Structure 4:531-541, 1996) that binding of the capsid protein residues 108 to 110 (the "N-terminal arm" residues) to a hydrophobic pocket on the surface of the neighboring capsid protein in the crystal structure mimics the binding of the E2 C-terminal residues into this pocket. In addition, structural comparisons of wild-type and mutant Sindbis virus capsid protein (SCP) and Semliki Forest virus capsid protein suggested that budding is associated with a switch between two conformations of the hydrophobic pocket. To test the proposed mechanism, SCP(114-264), which is missing the N-terminal arm, was crystallized to examine the pocket conformation when the pocket is empty. However, the pocket was occupied by dioxane molecules from the crystallization solution. The pocket conformation was the same as that when it was occupied by the N-terminal arm, demonstrating that the pocket favors binding ligands of appropriate size and shape. PubMed: 9779796DOI: 10.1002/(SICI)1097-0134(19981101)33:2<311::AID-PROT13>3.3.CO;2-L PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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