9EZB

SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P67S

• PDB DOI: https://doi.org/10.2210/pdb9EZB/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.237 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Starting Model: experimental

Literature

Structure of N-terminal domain mutant P67S of nucleocapsid protein of SARS-CoV-2

Dhamotharan, K., Schlundt, A., Guenther, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 59.68 kDa 
• Atom Count: 4,375 
• Modelled Residue Count: 505 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.237 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.789	α = 90
b = 92.466	β = 90
c = 96.393	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
REFMAC	refinement
PDB-REDO	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., Guenther, S.

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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