6NUT

Ebola virus nucleoprotein - RNA complex

• PDB DOI: https://doi.org/10.2210/pdb6NUT/pdb
• EM Map EMD-0522: EMDB EMDataResource
• NAKB: 6NUT

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Ebola virus - Mayinga, Zaire, 1976, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-02-01 Released: 2019-05-01 
• Deposition Author(s): Kirchdoerfer, R.N., Ward, A.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex.

Kirchdoerfer, R.N., Saphire, E.O., Ward, A.B.

(2019) Acta Crystallogr F Struct Biol Commun 75: 340-347

• PubMed: 31045563 
• DOI: https://doi.org/10.1107/S2053230X19004424
• Primary Citation of Related Structures:  
  6NUT


• PubMed Abstract: 
  

  Ebola virus is an emerging virus that is capable of causing a deadly disease in humans. Replication, transcription and packaging of the viral genome are carried out by the viral nucleocapsid. The nucleocapsid is a complex of the viral nucleoprotein, RNA and several other viral proteins. The nucleoprotein forms large, RNA-bound, helical filaments and acts as a scaffold for additional viral proteins. The 3.1 Å resolution single-particle cryo-electron microscopy structure of the nucleoprotein-RNA helical filament presented here resembles previous structures determined at lower resolution, while providing improved molecular details of protein-protein and protein-RNA interactions. The higher resolution of the structure presented here will facilitate the design and characterization of novel and specific Ebola virus therapeutics targeting the nucleocapsid.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 50-mer - A50 

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

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 52.2 kDa 
• Atom Count: 3,123 
• Modelled Residue Count: 385 
• Deposited Residue Count: 456 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	450	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 0  Gene Names: NP
UniProt
Find proteins for P18272 (Zaire ebolavirus (strain Mayinga-76)) Explore P18272  Go to UniProtKB:  P18272

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')	B [auth D]	6	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta	3.10
MODEL REFINEMENT	PHENIX	1.14rc3-3199
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Kirchdoerfer, R.N., Ward, A.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI123498
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Database references
• Version 1.2: 2019-11-13
  Changes: Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description