2JQM | pdb_00002jqm

Yellow Fever Envelope Protein Domain III NMR Structure (S288-K398)

• PDB DOI: https://doi.org/10.2210/pdb2JQM/pdb

• Classification: TRANSFERASE
• Organism(s): Yellow fever virus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-03 Released: 2008-06-10 
• Deposition Author(s): Volk, D.E., Gandham, S.H., May, F.J., Anderson, A., Barrett, A.D., Gorenstein, D.G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 19 
• Selection Criteria: structures with the least restraint violations 

Literature

Structure of yellow fever virus envelope protein domain III.

Volk, D.E., May, F.J., Gandham, S.H., Anderson, A., Von Lindern, J.J., Beasley, D.W., Barrett, A.D., Gorenstein, D.G.

(2009) Virology 394: 12-18

• PubMed: 19818466 
• DOI: https://doi.org/10.1016/j.virol.2009.09.001
• Primary Citation Related Structures: 
  2JQM


• PubMed Abstract: 
  

  The structure of recombinant domain III of the envelope protein (rED3) of yellow fever virus (YFV), containing the major neutralization site, was determined using NMR spectroscopy. The amino acid sequence and structure of the YFV-rED3 shows differences from ED3s of other mosquito-borne flaviviruses; in particular, the partially surface-exposed BC loop where methionine-304 and valine-324 were identified as being critical for the structure of the loop. Variations in the structure and surface chemistry of ED3 between flaviviruses affect neutralization sites and may affect host cell receptor interactions and play a role in the observed variations in viral pathogenesis and tissue tropism.

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Organizational Affiliation: 
• Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1157, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.95 kDa 
• Atom Count: 835 
• Modeled Residue Count: 112 
• Deposited Residue Count: 112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	A	112	Yellow fever virus	Mutation(s): 1
UniProt
Find proteins for Q6DV88 (Yellow fever virus (strain Ghana/Asibi/1927)) Explore Q6DV88  Go to UniProtKB:  Q6DV88

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 19 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-10 
Deposition Author(s): Volk, D.E., Gandham, S.H., May, F.J., Anderson, A., Barrett, A.D., Gorenstein, D.G.

Revision History  

• Version 1.0: 2008-06-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-12-20
  Changes: Data collection, Other
• Version 1.4: 2024-10-30
  Changes: Structure summary