Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (I)

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

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Identification of a guanine-specific pocket in the protein N of SARS-CoV-2.

Rafael Ciges-Tomas, J.Franco, M.L.Vilar, M.

(2022) Commun Biol 5: 711-711

  • DOI: https://doi.org/10.1038/s42003-022-03647-8
  • Primary Citation of Related Structures:  
    7O05, 7O35, 7O36

  • PubMed Abstract: 

    The SARS-CoV-2 nucleocapsid protein (N) is responsible for RNA binding. Here we report the crystal structure of the C-terminal domain (N CTD ) in open and closed conformations and in complex with guanine triphosphate, GTP. The crystal structure and biochemical studies reveal a specific interaction between the guanine, a nucleotide enriched in the packaging signals regions of coronaviruses, and a highly conserved tryptophan residue (W330). In addition, EMSA assays with SARS-CoV-2 derived RNA hairpin loops from a putative viral packaging sequence showed the preference interaction of the N-CTD to RNA oligonucleotides containing G and the loss of the specificity in the mutant W330A. Here we propose that this interaction may facilitate the viral assembly process. In summary, we have identified a specific guanine-binding pocket in the N protein that may be used to design viral assembly inhibitors.

  • Organizational Affiliation

    Instituto de Biomedicina de Valencia-CSIC Spanish National Research Council, C/Jaime Roig, 11, 46010, Valencia, Spain. rafaelciges@gmail.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
136Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
C10 H16 N5 O14 P3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.773α = 90
b = 92.719β = 90.01
c = 68.728γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainCOV20/01265

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description