Crystal structure of RNA-binding domain of nucleocapsid phosphoprotein from SARS CoV-2, monoclinic crystal form

Experimental Data Snapshot

  • Resolution: 2.67 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.

Kim, Y.Maltseva, N.Tesar, C.Jedrzejczak, R.Endres, M.Ma, H.Dugan, H.L.Stamper, C.T.Chang, C.Li, L.Changrob, S.Zheng, N.Y.Huang, M.Ramanathan, A.Wilson, P.Michalska, K.Joachimiak, A.

(2024) iScience 27: 108976-108976

  • DOI: https://doi.org/10.1016/j.isci.2024.108976
  • Primary Citation of Related Structures:  
    6VYO, 6WKP, 7N3C, 7N3D, 7STR, 7STS, 7SUE

  • PubMed Abstract: 

    Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NP RBD ) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NP RBD were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NP RBD complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA.

  • Organizational Affiliation

    Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10021, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
128Severe 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
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.388α = 90
b = 71.848β = 92.98
c = 106.961γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SBC-Collectdata collection
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2021-01-27
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-02-28
    Changes: Database references