Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.07 kDa 
• Atom Count: 3974 
• Modelled Residue Count: 472 
• Deposited Residue Count: 506 
• Unique protein chains: 1

4ILD

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

• PDB DOI: 10.2210/pdb4ILD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bovine viral diarrhea virus 1-NADL
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2012-12-30 Released: 2013-04-10 
• Deposition Author(s): Modis, Y., Li, Y., Wang, J.

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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 

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

• PubMed: 23569276 
• 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, 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein E2	A, B	253	Bovine viral diarrhea virus 1-NADL	Mutation(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)
UniProt
Find proteins for P19711 (Bovine viral diarrhea virus (isolate NADL)) Explore P19711  Go to UniProtKB:  P19711

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D 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
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IUM	O [auth B], P [auth B], Q [auth B], R [auth B]	URANYL (VI) ION O2 U IZLHQJIUOZHTLW-UHFFFAOYSA-N
CA	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 
• 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 = 136.72	α = 90
b = 54.45	β = 92.23
c = 95.92	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
MLPHARE	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-30 
• Released Date: 2013-04-10 
Deposition Author(s): Modis, Y., Li, Y., Wang, J.

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