4UD1

Structure of the N Terminal domain of the MERS CoV nucleocapsid

• PDB DOI: https://doi.org/10.2210/pdb4UD1/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Middle East respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-05 Released: 2015-12-02 
• Deposition Author(s): Papageorgiou, N., Lichiere, J., Ferron, F., Canard, B., Coutard, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.274 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

Literature

Structural Characterization of the N-Terminal Part of the Mers-Cov Nucleocapsid by X-Ray Diffraction and Small-Angle X-Ray Scattering

Papageorgiou, N., Lichiere, J., Baklouti, A., Ferron, F., Canard, B., Coutard, B.

(2016) Acta Crystallogr D Biol Crystallogr 72: 192

• PubMed: 26894667 
• DOI: https://doi.org/10.1107/S2059798315024328
• Primary Citation of Related Structures:  
  4UD1


• PubMed Abstract: 
  

  The N protein of coronaviruses is a multifunctional protein that is organized into several domains. The N-terminal part is composed of an intrinsically disordered region (IDR) followed by a structured domain called the N-terminal domain (NTD). In this study, the structure determination of the N-terminal region of the MERS-CoV N protein via X-ray diffraction measurements is reported at a resolution of 2.4 Å. Since the first 30 amino acids were not resolved by X-ray diffraction, the structural study was completed by a SAXS experiment to propose a structural model including the IDR. This model presents the N-terminal region of the MERS-CoV as a monomer that displays structural features in common with other coronavirus NTDs.

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Organizational Affiliation: 

CNRS, AFMB UMR 7257, 13288 Marseille, France.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.53 kDa 
• Atom Count: 4,922 
• Modelled Residue Count: 621 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N PROTEIN	A, B, C, D, E	164	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0
UniProt
Find proteins for T2B9R0 (Middle East respiratory syndrome-related coronavirus) Explore T2B9R0  Go to UniProtKB:  T2B9R0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth B], L [auth C], M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	H [auth B], K [auth C]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
NH4	F [auth A], G [auth B], J [auth C], N [auth E]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.274 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.648	α = 90
b = 67.021	β = 89.98
c = 60.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Papageorgiou, N., Lichiere, J., Ferron, F., Canard, B., Coutard, B.

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2016-02-03
  Changes: Data collection
• Version 1.2: 2016-02-10
  Changes: Database references
• Version 1.3: 2016-03-02
  Changes: Database references
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description