1WYK

SINDBIS VIRUS CAPSID PROTEIN (114-264)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Probing the potential glycoprotein binding site of sindbis virus capsid protein with dioxane and model building.

Lee, S.Kuhn, R.J.Rossmann, M.G.

(1998) Proteins 33: 311-317


  • 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 re ...

    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.


    Related Citations: 
    • Identification of a Protein Binding Site on the Surface of the Alphavirus Nucleocapsid and its Implication in Virus Assembly
      Lee, S.,Owen, K.E.,Choi, H.K.,Lee, H.,Lu, G.,Wengler, G.,Brown, D.T.,Rossmann, M.G.,Kuhn, R.J.
      (1996) Structure 4: 531
    • Structure of Sindbis Virus Core Protein Reveals a Chymotrypsin-Like Serine Proteinase and the Organization of the Virion
      Choi, H.K.,Tong, L.,Minor, W.,Dumas, P.,Boege, U.,Rossmann, M.G.,Wengler, G.
      (1991) Nature 354: 37


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SINDBIS VIRUS CAPSID PROTEIN
A, B, C, D
152Sindbis virus subtype Ockelbo (strain Edsbyn 82-5)EC: 3.4.21.90
Find proteins for P27285 (Sindbis virus subtype Ockelbo (strain Edsbyn 82-5))
Go to UniProtKB:  P27285
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DIO
Query on DIO

Download SDF File 
Download CCD File 
A, B, C, D
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
FOR
Query on FOR

Download SDF File 
Download CCD File 
A, B, C, D
FORMYL GROUP
C H2 O
WSFSSNUMVMOOMR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.197 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 35.980α = 109.40
b = 59.540β = 101.50
c = 71.050γ = 90.14
Software Package:
Software NamePurpose
X-PLORmodel building
HKLdata reduction
X-PLORphasing
X-PLORrefinement
HKLdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance