4ILD

Crystal structure of truncated Bovine viral diarrhea virus 1 E2 envelope protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of glycoprotein E2 from bovine viral diarrhea virus.

Li, Y., Wang, J., Kanai, R., Modis, Y.

(2013) Proc Natl Acad Sci U S A 110: 6805-6810

  • DOI: 10.1073/pnas.1300524110
  • Primary Citation of Related Structures:  
    4ILD, 4JNT

  • PubMed Abstract: 

    • Pestiviruses, including bovine viral diarrhea virus, are important animal pathogens and are closely related to hepatitis C virus, which remains a major global health threat. They have an outer lipid envelope bearing two glycoproteins, E1 and E2, requ ...

    Pestiviruses, including bovine viral diarrhea virus, are important animal pathogens and are closely related to hepatitis C virus, which remains a major global health threat. They have an outer lipid envelope bearing two glycoproteins, E1 and E2, required for cell entry. They deliver their genome into the host cell cytoplasm by fusion of their envelope with a cellular membrane. The crystal structure of bovine viral diarrhea virus E2 reveals a unique protein architecture consisting of two Ig-like domains followed by an elongated β-stranded domain with a new fold. E2 forms end-to-end homodimers with a conserved C-terminal motif rich in aromatic residues at the contact. A disulfide bond across the interface explains the acid resistance of pestiviruses and their requirement for a redox activation step to initiate fusion. From the structure of E2, we propose alternative possible membrane fusion mechanisms. We expect the pestivirus fusion apparatus to be conserved in hepatitis C virus.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein E2A, B253Bovine viral diarrhea virus 1-NADLMutation(s): 0 
EC: 3.4.22 (UniProt), 3.4.21.113 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P19711 (Bovine viral diarrhea virus (isolate NADL))
Explore P19711 
Go to UniProtKB:  P19711
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F, G, H, I, J
2 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IUM
Query on IUM
Download CCD File 
B
URANYL (VI) ION
O2 U
IZLHQJIUOZHTLW-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/62 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.72α = 90
b = 54.45β = 92.23
c = 95.92γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
MLPHAREphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references
  • Version 1.2: 2013-05-08
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary