9RCZ | pdb_00009rcz

Structure of the N-terminal domain of non-structural protein 1 (Nsp1) from SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb9RCZ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-30 Released: 2025-07-09 
• Deposition Author(s): Lennartz, F., Weiss, M.S.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystallographic fragment screening against SARS-CoV-2 Nsp1 using the F2X-Entry Screen and a newly developed fragment library.

Lennartz, F., Wollenhaupt, J., Oelker, M., Froeling, P., Mueller, U., Deckers, A., Grathwol, C., Braese, S., Jung, N., Weiss, M.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.73 kDa 
• Atom Count: 982 
• Modeled Residue Count: 113 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1a polyprotein	A [auth B]	115	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: ORF1ab
UniProt
Find proteins for A0A8B1K137 (Severe acute respiratory syndrome coronavirus 2) Explore A0A8B1K137  Go to UniProtKB:  A0A8B1K137

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.75	α = 90
b = 36.75	β = 90
c = 142.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Lennartz, F., Weiss, M.S.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	FISCOV Innovationspool

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release