3C6E | pdb_00003c6e

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.293 (Depositor) 
  • R-Value Work: 
    0.250 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3C6E

Ligand Structure Quality Assessment 


This is version 2.3 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: https://doi.org/10.1126/science.1153263
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 60.86 kDa 
  • Atom Count: 3,811 
  • Modeled Residue Count: 471 
  • Deposited Residue Count: 532 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope protein E402Dengue virus 2 Thailand/16681/84Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O11875 (Dengue virus type 2)
Explore O11875 
Go to UniProtKB:  O11875
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO11875
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
prMB [auth C]130dengue virus type 2Mutation(s): 3 
Membrane Entity: Yes 
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
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G49078BH
GlyCosmos: G49078BH
GlyGen: G49078BH

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NDG

Query on NDG



Download:Ideal Coordinates CCD File
D [auth C]2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.293 (Depositor) 
  • R-Value Work:  0.250 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.104α = 90
b = 108.366β = 90
c = 108.956γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: Source and taxonomy, Version format compliance
  • 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, Structure summary
  • Version 2.2: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-13
    Changes: Structure summary