Biological Assembly 1  

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

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 27.29 kDa 
• Atom Count: 2223 
• Modelled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

4J4R

Hexameric SFTSVN

• PDB DOI: 10.2210/pdb4J4R/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Phlebovirus JS2010-018
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-07 Released: 2013-05-22 
• Deposition Author(s): Jiao, L., Ouyang, S., Liang, M., Niu, F., Shaw, N., Wu, W., Ding, W., Jin, C., Zhu, Y., Zhang, F., Wang, T., Li, C., Zuo, X., Luan, C.H., Li, D., Liu, Z.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

Structure of severe Fever with thrombocytopenia syndrome virus nucleocapsid protein in complex with suramin reveals therapeutic potential

Jiao, L., Ouyang, S., Liang, M., Niu, F., Shaw, N., Wu, W., Ding, W., Jin, C., Peng, Y., Zhu, Y., Zhang, F., Wang, T., Li, C., Zuo, X., Luan, C.H., Li, D., Liu, Z.J.

(2013) J Virol 87: 6829-6839

• PubMed: 23576501 
• DOI: 10.1128/JVI.00672-13
• Primary Citation of Related Structures:  
  4J4R, 4J4S, 4J4U, 4J4V, 4J4W, 4J4X, 4J4Y


• PubMed Abstract: 
  

Severe fever with thrombocytopenia syndrome is an emerging infectious disease caused by a novel bunyavirus (SFTSV). Lack of vaccines and inadequate therapeutic treatments have made the spread of the virus a global concern. Viral nucleocapsid protein (N) is essential for its transcription and replication. Here, we present the crystal structures of N from SFTSV and its homologs from Buenaventura (BUE) and Granada (GRA) viruses. The structures reveal that phleboviral N folds into a compact core domain and an extended N-terminal arm that mediates oligomerization, such as tetramer, pentamer, and hexamer of N assemblies. Structural superimposition indicates that phleboviral N adopts a conserved architecture and uses a similar RNA encapsidation strategy as that of RVFV-N. The RNA binding cavity runs along the inner edge of the ring-like assembly. A triple mutant of SFTSV-N, R64D/K67D/K74D, almost lost its ability to bind RNA in vitro, is deficient in its ability to transcribe and replicate. Structural studies of the mutant reveal that both alterations in quaternary assembly and the charge distribution contribute to the loss of RNA binding. In the screening of inhibitors Suramin was identified to bind phleboviral N specifically. The complex crystal structure of SFTSV-N with Suramin was refined to a 2.30-Å resolution. Suramin was found sitting in the putative RNA binding cavity of SFTSV-N. The inhibitory effect of Suramin on SFTSV replication was confirmed in Vero cells. Therefore, a common Suramin-based therapeutic approach targeting SFTSV-N and its homologs could be developed for containing phleboviral outbreaks.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleocapsid protein	A	248	Phlebovirus JS2010-018	Mutation(s): 0
UniProt
Find proteins for I6WJ72 (Phlebovirus JS2010-018) Explore I6WJ72  Go to UniProtKB:  I6WJ72

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.995	α = 90
b = 103.995	β = 90
c = 48.866	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-07 
• Released Date: 2013-05-22 
Deposition Author(s): Jiao, L., Ouyang, S., Liang, M., Niu, F., Shaw, N., Wu, W., Ding, W., Jin, C., Zhu, Y., Zhang, F., Wang, T., Li, C., Zuo, X., Luan, C.H., Li, D., Liu, Z.J.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references