4ILD | pdb_00004ild

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 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

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: https://doi.org/10.1073/pnas.1300524110
  • Primary Citation 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, 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.

Macromolecule Content 

  • Total Structure Weight: 62.07 kDa 
  • Atom Count: 3,974 
  • Modeled Residue Count: 472 
  • Deposited Residue Count: 506 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein E2
A, B
253Bovine viral diarrhea virus 1-NADLMutation(s): 0 
UniProt
Find proteins for P19711 (Bovine viral diarrhea virus (isolate NADL))
Explore P19711 
Go to UniProtKB:  P19711
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19711
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F, G
C, D, E, F, G, H, I, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

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

Query on IUM



Download:Ideal Coordinates CCD File
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
URANYL (VI) ION
O2 U
IZLHQJIUOZHTLW-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A],
M [auth A],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free:  0.289 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: C 1 2 1
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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary