9F5L

SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant A119S

• PDB DOI: https://doi.org/10.2210/pdb9F5L/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-04-29 Released: 2024-11-20 
• Deposition Author(s): Dhamotharan, K., Schlundt, A.
• Funding Organization(s): German Research Foundation (DFG), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.323 
• R-Value Work: 0.314 
• R-Value Observed: 0.314 

Starting Model: experimental

Literature

Structure of N-terminal domain mutant A119S of nucleocapsid protein of SARS-CoV-2

Dhamotharan, K., Schlundt, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.64 kDa 
• Atom Count: 3,998 
• Modelled Residue Count: 495 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D	136	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1
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: 2.36 Å
• R-Value Free: 0.323 
• R-Value Work: 0.314 
• R-Value Observed: 0.314 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.871	α = 90
b = 92.203	β = 90
c = 99.166	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Coot	model building
BUCCANEER	model building
Aimless	data scaling
pointless	data scaling
STARANISO	data scaling
autoPROC	data reduction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Dhamotharan, K., Schlundt, A.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SCHL2062/2-1 and 2-2
German Research Foundation (DFG)	Germany	161793742
Other government		Goethe-Corona-Funds
Other government		Johanna Quandt Young Academy at Goethe (stipend number 2019/AS01)

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release