4DVK

Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 strain NCP-7

• PDB DOI: https://doi.org/10.2210/pdb4DVK/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bovine viral diarrhea virus 1-CP7
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2012-02-23 Released: 2012-05-23 
• Deposition Author(s): Krey, T., Bontems, F., Vonrhein, C., Vaney, M.-C., Bricogne, G., Ruemenapf, T., Rey, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.225 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.39 kDa 
• Atom Count: 3,193 
• Modelled Residue Count: 314 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E(rns) glycoprotein	A, B	165	Bovine viral diarrhea virus 1-CP7	Mutation(s): 0  Gene Names: Erns
UniProt
Find proteins for Q96662 (Bovine viral diarrhea virus (strain CP7)) Explore Q96662  Go to UniProtKB:  Q96662

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G51778NN GlyCosmos:  G51778NN GlyGen:  G51778NN

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21477HL GlyCosmos:  G21477HL GlyGen:  G21477HL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.225 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.04	α = 90
b = 106.04	β = 90
c = 211.85	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
SHARP	phasing
SOLOMON	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Krey, T., Bontems, F., Vonrhein, C., Vaney, M.-C., Bricogne, G., Ruemenapf, T., Rey, F.A.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary