7STS

Crystal Structure of Human Fab S24-1379 in the Complex with the N-teminal Domain of Nucleocapsid Protein from SARS CoV-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.200 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

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

    Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab S24-1379, heavy chainA,
E [auth H]
218Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab S24-1379, light chainB,
F [auth L]
212Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein
C, D
130Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.200 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.084α = 90
b = 99.084β = 90
c = 221.89γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
xia2data reduction
HKL-3000phasing
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 2.0: 2022-08-17
    Changes: Advisory, Atomic model
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references
  • Version 2.2: 2024-04-03
    Changes: Refinement description