6YUN | pdb_00006yun

1.45 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb6YUN/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-27 Released: 2020-05-20 
• Deposition Author(s): Zinzula, L., Basquin, J., Nagy, I., Bracher, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.189 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

High-resolution structure and biophysical characterization of the nucleocapsid phosphoprotein dimerization domain from the Covid-19 severe acute respiratory syndrome coronavirus 2.

Zinzula, L., Basquin, J., Bohn, S., Beck, F., Klumpe, S., Pfeifer, G., Nagy, I., Bracher, A., Hartl, F.U., Baumeister, W.

(2021) Biochem Biophys Res Commun 538: 54-62

• PubMed: 33039147 
• DOI: https://doi.org/10.1016/j.bbrc.2020.09.131
• Primary Citation Related Structures: 
  6YUN, 6ZCO


• PubMed Abstract: 
  

  Unprecedented by number of casualties and socio-economic burden occurring worldwide, the coronavirus disease 2019 (Covid-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the worst health crisis of this century. In order to develop adequate countermeasures against Covid-19, identification and structural characterization of suitable antiviral targets within the SARS-CoV-2 protein repertoire is urgently needed. The nucleocapsid phosphoprotein (N) is a multifunctional and highly immunogenic determinant of virulence and pathogenicity, whose main functions consist in oligomerizing and packaging the single-stranded RNA (ssRNA) viral genome. Here we report the structural and biophysical characterization of the SARS-CoV-2 N C-terminal domain (CTD), on which both N homo-oligomerization and ssRNA binding depend. Crystal structures solved at 1.44 Å and 1.36 Å resolution describe a rhombus-shape N CTD dimer, which stably exists in solution as validated by size-exclusion chromatography coupled to multi-angle light scattering and analytical ultracentrifugation. Differential scanning fluorimetry revealed moderate thermal stability and a tendency towards conformational change. Microscale thermophoresis demonstrated binding to a 7-bp SARS-CoV-2 genomic ssRNA fragment at micromolar affinity. Furthermore, a low-resolution preliminary model of the full-length SARS-CoV N in complex with ssRNA, obtained by cryo-electron microscopy, provides an initial understanding of self-associating and RNA binding functions exerted by the SARS-CoV-2 N.

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Organizational Affiliation: 
• The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany. Electronic address: [e-mail].
The Max-Planck Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152, Martinsried, Germany.
The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany; The Max-Planck Institute of Biochemistry, Department of Cellular Machines and Signaling, Am Klopferspitz 18, 82152, Martinsried, Germany.
The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany.
The Max-Planck Institute of Biochemistry, Department of Cellular Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.25 kDa 
• Atom Count: 2,381 
• Modeled Residue Count: 251 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B	135	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.189 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.43	α = 90
b = 46.856	β = 90
c = 131.947	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Zinzula, L., Basquin, J., Nagy, I., Bracher, A.

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2021-03-03
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description