3U3I | pdb_00003u3i

A RNA binding protein from Crimean-Congo hemorrhagic fever virus

• PDB DOI: https://doi.org/10.2210/pdb3U3I/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Orthonairovirus haemorrhagiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-06 Released: 2012-03-28 
• Deposition Author(s): Guo, Y., Wang, W.M., Ji, W., Deng, M., Sun, Y.N., Lou, Z.Y., Rao, Z.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.257 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Crimean-Congo hemorrhagic fever virus nucleoprotein reveals endonuclease activity in bunyaviruses

Guo, Y., Wang, W.M., Ji, W., Deng, M., Sun, Y.N., Zhou, H., Yang, C., Deng, F., Wang, H., Hu, Z., Lou, Z.Y., Rao, Z.H.

(2012) Proc Natl Acad Sci U S A 109: 5046-5051

• PubMed: 22421137 
• DOI: https://doi.org/10.1073/pnas.1200808109
• Primary Citation Related Structures: 
  3U3I


• PubMed Abstract: 
  

  Crimean-Congo hemorrhagic fever virus (CCHFV), a virus with high mortality in humans, is a member of the genus Nairovirus in the family Bunyaviridae, and is a causative agent of severe hemorrhagic fever (HF). It is classified as a biosafety level 4 pathogen and a potential bioterrorism agent due to its aerosol infectivity and its ability to cause HF outbreaks with high case fatality (∼30%). However, little is known about the structural features and function of nucleoproteins (NPs) in the Bunyaviridae, especially in CCHFV. Here we report a 2.3-Å resolution crystal structure of the CCHFV nucleoprotein. The protein has a racket-shaped overall structure with distinct "head" and "stalk" domains and differs significantly with NPs reported so far from other negative-sense single-stranded RNA viruses. Furthermore, CCHFV NP shows a distinct metal-dependent DNA-specific endonuclease activity. Single residue mutations in the predicted active site resulted in a significant reduction in the observed endonuclease activity. Our results present a new folding mechanism and function for a negative-strand RNA virus nucleoprotein, extend our structural insight into bunyavirus NPs, and provide a potential target for antiviral drug development to treat CCHFV infection.

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Organizational Affiliation: 
• Laboratory of Structural Biology, School of Medicine and Life Sciences, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 53.98 kDa 
• Atom Count: 3,995 
• Modeled Residue Count: 460 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleocapsid protein	A	482	Orthonairovirus haemorrhagiae	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P89522 (Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)) Explore P89522  Go to UniProtKB:  P89522

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.257 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.339	α = 90
b = 67.898	β = 90
c = 131.506	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Guo, Y., Wang, W.M., Ji, W., Deng, M., Sun, Y.N., Lou, Z.Y., Rao, Z.H.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references