1R6R

Solution Structure of Dengue Virus Capsid Protein Reveals a New Fold


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 54 
  • Conformers Submitted: 21 
  • Selection Criteria: 20 arbitrarily selected from 53/54 conformers with no constraint violations larger than 0.3 angstrom or 5 degrees. model 21 is energy minimized structure averaged over the 53 models. 

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This is version 1.2 of the entry. See complete history


Literature

Solution structure of dengue virus capsid protein reveals another fold

Ma, L.Jones, C.T.Groesch, T.D.Kuhn, R.J.Post, C.B.

(2004) Proc Natl Acad Sci U S A 101: 3414-3419

  • DOI: 10.1073/pnas.0305892101
  • Primary Citation of Related Structures:  
    1R6R

  • PubMed Abstract: 
  • Dengue virus is responsible for approximately 50-100 million infections, resulting in nearly 24,000 deaths annually. The capsid (C) protein of dengue virus is essential for specific encapsidation of the RNA genome, but little structural information on the C protein is available ...

    Dengue virus is responsible for approximately 50-100 million infections, resulting in nearly 24,000 deaths annually. The capsid (C) protein of dengue virus is essential for specific encapsidation of the RNA genome, but little structural information on the C protein is available. We report the solution structure of the 200-residue homodimer of dengue 2 C protein. The structure provides, to our knowledge, the first 3D picture of a flavivirus C protein and identifies a fold that includes a large dimerization surface contributed by two pairs of helices, one of which has characteristics of a coiled-coil. NMR structure determination involved a secondary structure sorting approach to facilitate assignment of the intersubunit nuclear Overhauser effect interactions. The dimer of dengue C protein has an unusually high net charge, and the structure reveals an asymmetric distribution of basic residues over the surface of the protein. Nearly half of the basic residues lie along one face of the dimer. In contrast, the conserved hydrophobic region forms an extensive apolar surface at a dimer interface on the opposite side of the molecule. We propose a model for the interaction of dengue C protein with RNA and the viral membrane that is based on the asymmetric charge distribution of the protein and is consistent with previously reported results.


    Organizational Affiliation

    Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinA, B100Dengue virus 2 Puerto Rico/PR159-S1/1969Mutation(s): 0 
Gene Names: Capsid Gene
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P12823 (Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969))
Explore P12823 
Go to UniProtKB:  P12823
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 54 
  • Conformers Submitted: 21 
  • Selection Criteria: 20 arbitrarily selected from 53/54 conformers with no constraint violations larger than 0.3 angstrom or 5 degrees. model 21 is energy minimized structure averaged over the 53 models. 
  • OLDERADO: 1R6R Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance