7STS | pdb_00007sts

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

• PDB DOI: https://doi.org/10.2210/pdb7STS/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-11-15 Released: 2022-08-10 
• Deposition Author(s): Kim, Y., Maltseva, N., Tesar, C., Jedrzejczak, R., Dugan, H., Stamper, C., Wilson, P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

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

• PubMed: 38327783 
• DOI: https://doi.org/10.1016/j.isci.2024.108976
• Primary Citation 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.

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Organizational Affiliation: 
• Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA.
Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 120.09 kDa 
• Atom Count: 8,245 
• Modeled Residue Count: 1,074 
• Deposited Residue Count: 1,120 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab S24-1379, heavy chain	A, E [auth H]	218	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab S24-1379, light chain	B, F [auth L]	212	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	C, D	130	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: 2.16 Å
• R-Value Free:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.084	α = 90
b = 99.084	β = 90
c = 221.89	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
xia2	data reduction
HKL-3000	phasing
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Kim, Y., Maltseva, N., Tesar, C., Jedrzejczak, R., Dugan, H., Stamper, C., Wilson, P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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

Revision History  

• 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
• Version 2.3: 2024-11-20
  Changes: Structure summary