Structure of the SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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This is version 1.3 of the entry. See complete history


Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies.

Ye, Q.Lu, S.Corbett, K.D.

(2021) Front Immunol 12: 719037-719037

  • DOI: https://doi.org/10.3389/fimmu.2021.719037
  • Primary Citation of Related Structures:  
    7N0I, 7N0R, 7R98

  • PubMed Abstract: 

    The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, is the most severe public health event of the twenty-first century. While effective vaccines against SARS-CoV-2 have been developed, there remains an urgent need for diagnostics to quickly and accurately detect infections. Antigen tests, particularly those that detect the abundant SARS-CoV-2 Nucleocapsid protein, are a proven method for detecting active SARS-CoV-2 infections. Here we report high-resolution crystal structures of three llama-derived single-domain antibodies that bind the SARS-CoV-2 Nucleocapsid protein with high affinity. Each antibody recognizes a specific folded domain of the protein, with two antibodies recognizing the N-terminal RNA binding domain and one recognizing the C-terminal dimerization domain. The two antibodies that recognize the RNA binding domain affect both RNA binding affinity and RNA-mediated phase separation of the Nucleocapsid protein. All three antibodies recognize highly conserved surfaces on the Nucleocapsid protein, suggesting that they could be used to develop affordable diagnostic tests to detect all circulating SARS-CoV-2 variants.

  • Organizational Affiliation

    Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein96Severe 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Single-domain antibody E2H [auth I],
I [auth J],
J [auth K],
K [auth L]
139Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.846α = 90
b = 131.557β = 90
c = 140.048γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM128464

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2022-02-09
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description