Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.13 kDa 
• Atom Count: 2512 
• Residue Count: 293 
• Unique protein chains: 1

4Z9P

Crystal structure of Ebola virus nucleoprotein core domain at 1.8A resolution

• DOI: 10.2210/pdb4Z9P/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Ebola virus - Mayinga, Zaire, 1976
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-11 Released: 2015-05-20 
• Deposition Author(s): Guo, Y., Dong, S.S., Yang, P., Li, G.B., Liu, B.C., Yang, C., Rao, Z.H.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Literature

Insight into the Ebola virus nucleocapsid assembly mechanism: crystal structure of Ebola virus nucleoprotein core domain at 1.8 A resolution.

Dong, S., Yang, P., Li, G., Liu, B., Wang, W., Liu, X., Xia, B., Yang, C., Lou, Z., Guo, Y., Rao, Z.

(2015) Protein Cell 6: 351-362

• PubMed: 25910597 
• DOI: 10.1007/s13238-015-0163-3
• Primary Citation of Related Structures:  
  4Z9P


• PubMed Abstract: 
  

Ebola virus (EBOV) is a key member of Filoviridae family and causes severe human infectious diseases with high morbidity and mortality. As a typical negative-sense single-stranded RNA (-ssRNA) viruses, EBOV possess a nucleocapsid protein (NP) to facilitate genomic RNA encapsidation to form viral ribonucleoprotein complex (RNP) together with genome RNA and polymerase, which plays the most essential role in virus proliferation cycle. However, the mechanism of EBOV RNP formation remains unclear. In this work, we solved the high resolution structure of core domain of EBOV NP. The polypeptide of EBOV NP core domain (NP(core)) possesses an N-lobe and C-lobe to clamp a RNA binding groove, presenting similarities with the structures of the other reported viral NPs encoded by the members from Mononegavirales order. Most strikingly, a hydrophobic pocket at the surface of the C-lobe is occupied by an α-helix of EBOV NP(core) itself, which is highly conserved among filoviridae family. Combined with other biochemical and biophysical evidences, our results provides great potential for understanding the mechanism underlying EBOV RNP formation via the mobility of EBOV NP element and enables the development of antiviral therapies targeting EBOV RNP formation.

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Organizational Affiliation: 

State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300071, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	317	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 0  Gene Names: NP
Find proteins for P18272 (Zaire ebolavirus (strain Mayinga-76)) Explore P18272  Go to UniProtKB:  P18272

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.845	α = 90
b = 162.877	β = 90
c = 31.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-04-11 
• Released Date: 2015-05-20 
Deposition Author(s): Guo, Y., Dong, S.S., Yang, P., Li, G.B., Liu, B.C., Yang, C., Rao, Z.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31300606

Revision History 

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2015-06-03
  Changes: Data collection
• Version 1.2: 2017-10-18
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy