Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 180-mer - A180 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 129.07 kDa 
• Atom Count: 8122 
• Residue Count: 1046 
• Unique protein chains: 1

4NWV

Crystal structure of Orsay virus-like particle

• DOI: 10.2210/pdb4NWV/pdb

• Classification: VIRUS
• Organism(s): Orsay virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-06 Released: 2014-08-20 
• Deposition Author(s): Tao, Y.J., Guo, Y.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.279 
• R-Value Work: 0.278 
• R-Value Observed: 0.278 

Literature

Crystal structure of a nematode-infecting virus.

Guo, Y.R., Hryc, C.F., Jakana, J., Jiang, H., Wang, D., Chiu, W., Zhong, W., Tao, Y.J.

(2014) Proc Natl Acad Sci U S A 111: 12781-12786

• PubMed: 25136116 
• DOI: 10.1073/pnas.1407122111
• Primary Citation of Related Structures:  
  4NWV, 4NWW


• PubMed Abstract: 
  

Orsay, the first virus discovered to naturally infect Caenorhabditis elegans or any nematode, has a bipartite, positive-sense RNA genome. Sequence analyses show that Orsay is related to nodaviruses, but molecular characterizations of Orsay reveal several unique features, such as the expression of a capsid-δ fusion protein and the use of an ATG-independent mechanism for translation initiation. Here we report the crystal structure of an Orsay virus-like particle assembled from recombinant capsid protein (CP). Orsay capsid has a T = 3 icosahedral symmetry with 60 trimeric surface spikes. Each CP can be divided into three regions: an N-terminal arm that forms an extended protein interaction network at the capsid interior, an S domain with a jelly-roll, β-barrel fold forming the continuous capsid, and a P domain that forms surface spike projections. The structure of the Orsay S domain is best aligned to T = 3 plant RNA viruses but exhibits substantial differences compared with the insect-infecting alphanodaviruses, which also lack the P domain in their CPs. The Orsay P domain is remotely related to the P1 domain in calicivirus and hepatitis E virus, suggesting a possible evolutionary relationship. Removing the N-terminal arm produced a slightly expanded capsid with fewer nucleic acids packaged, suggesting that the arm is important for capsid stability and genome packaging. Because C. elegans-Orsay serves as a highly tractable model for studying viral pathogenesis, our results should provide a valuable structural framework for further studies of Orsay replication and infection.

---

Organizational Affiliation: 

Department of BioSciences, Rice University, Houston, TX 77005; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C	391	Orsay virus	Mutation(s): 0  Gene Names: Capsid Protein
Find proteins for E9KNV5 (Orsay virus) Explore E9KNV5  Go to UniProtKB:  E9KNV5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.279 
• R-Value Work: 0.278 
• R-Value Observed: 0.278 
• Space Group: I 2 2 2
• Diffraction Data DOI: 10.15785/SBGRID/9 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 402.197	α = 90
b = 369.862	β = 90
c = 410.511	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MD2	data collection
HKL-2000	data reduction
HKL-2000	data scaling
RAVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-06 
• Released Date: 2014-08-20 
Deposition Author(s): Tao, Y.J., Guo, Y.R.

Revision History 

• Version 1.0: 2014-08-20
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2015-12-02
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Refinement description