3C5X

Crystal structure of the precursor membrane protein- envelope protein heterodimer from the dengue 2 virus at low pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The flavivirus precursor membrane-envelope protein complex: structure and maturation.

Li, L.Lok, S.M.Yu, I.M.Zhang, Y.Kuhn, R.J.Chen, J.Rossmann, M.G.

(2008) Science 319: 1830-1834

  • DOI: 10.1126/science.1153263
  • Primary Citation of Related Structures:  
    3C5X, 3C6D, 3C6E

  • PubMed Abstract: 
  • Many viruses go through a maturation step in the final stages of assembly before being transmitted to another host. The maturation process of flaviviruses is directed by the proteolytic cleavage of the precursor membrane protein (prM), turning inert virus into infectious particles ...

    Many viruses go through a maturation step in the final stages of assembly before being transmitted to another host. The maturation process of flaviviruses is directed by the proteolytic cleavage of the precursor membrane protein (prM), turning inert virus into infectious particles. We have determined the 2.2 angstrom resolution crystal structure of a recombinant protein in which the dengue virus prM is linked to the envelope glycoprotein E. The structure represents the prM-E heterodimer and fits well into the cryo-electron microscopy density of immature virus at neutral pH. The pr peptide beta-barrel structure covers the fusion loop in E, preventing fusion with host cell membranes. The structure provides a basis for identifying the stages of its pH-directed conformational metamorphosis during maturation, ending with release of pr when budding from the host.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope protein EA402Dengue virus 2 Thailand/16681/84Mutation(s): 0 
UniProt
Find proteins for Q6H1E5 (Dengue virus type 2)
Explore Q6H1E5 
Go to UniProtKB:  Q6H1E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6H1E5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
prMB [auth C]130Dengue virus 2Mutation(s): 3 
UniProt
Find proteins for Q3BCY3 (Dengue virus type 2)
Explore Q3BCY3 
Go to UniProtKB:  Q3BCY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3BCY3
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-altropyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G43142BR
GlyCosmos:  G43142BR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.209α = 90
b = 108.595β = 90
c = 108.738γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2008-04-08 
  • Deposition Author(s): Li, L.

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2011-08-24
    Changes: Atomic model
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary