4XZE | pdb_00004xze

The crystal structure of Hazara virus nucleoprotein

• PDB DOI: https://doi.org/10.2210/pdb4XZE/pdb

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


• Deposited: 2015-02-04 Released: 2015-09-02 
• Deposition Author(s): Guo, Y., Wang, W., Liu, X., Wang, X., Wang, J., Huo, T., Liu, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.287 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Diversity of Nairovirus-Encoded Nucleoproteins.

Wang, W., Liu, X., Wang, X., Dong, H., Ma, C., Wang, J., Liu, B., Mao, Y., Wang, Y., Li, T., Yang, C., Guo, Y.

(2015) J Virol 89: 11740-11749

• PubMed: 26246561 
• DOI: https://doi.org/10.1128/JVI.01680-15
• Primary Citation Related Structures: 
  4XZ8, 4XZA, 4XZC, 4XZE


• PubMed Abstract: 
  

  The nairoviruses include assorted tick-borne bunyaviruses that are emerging as causative agents of infectious diseases among humans and animals. As negative-sense single-stranded RNA (-ssRNA) viruses, nairoviruses encode nucleoprotein (NP) that encapsidates the genomic RNA and further forms ribonucleoprotein (RNP) complex with viral RNA-dependent RNA polymerase (RdRp). We previously revealed that the monomeric NP encoded by Crimean-Congo hemorrhagic fever virus (CCHFV) presents a racket-shaped structure and shows unusual DNA-specific endonuclease activity. To examine the structural and biological variation of nairovirus-encoded NPs, here, we systematically solved the crystal structures of NPs encoded by various nairoviruses, including Hazara virus (HAZV), Kupe virus (KUPV), and Erve virus (ERVEV). Combined with biochemical analysis, our results generate a clearer picture to aid in the understanding of the functional diversity of nairovirus-encoded NPs and the formation of nairovirus RNPs. Nairoviruses comprise several tick-borne bunyaviruses that are emerging as causative agents of infectious diseases among humans and animals; however, little is known of the nairovirus genome assembly and transcription mechanisms. Based on the previous study of CCHFV NP reported by different research groups, we systematically investigate here the structural and functional diversity among three different nairoviruses. This work provides important information on nairovirus nucleoprotein function and the formation of RNPs.

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Organizational Affiliation: 
• State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China Institute of Molecular Science, Chemical Biology and Molecular Engineering Laboratory of Education Ministry, Shanxi University, Taiyuan, Shanxi, China.
Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China.
State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, People's Republic of China.
Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China.
State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China [e-mail] [e-mail].

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 218.18 kDa 
• Atom Count: 14,978 
• Modeled Residue Count: 1,885 
• Deposited Residue Count: 1,952 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D	488	Hazara virus	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P27318 (Hazara virus (isolate JC280)) Explore P27318  Go to UniProtKB:  P27318

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.287 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.404	α = 90
b = 72.17	β = 90
c = 453.669	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Guo, Y., Wang, W., Liu, X., Wang, X., Wang, J., Huo, T., Liu, B.

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2015-11-18
  Changes: Database references
• Version 1.2: 2020-02-05
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description