9P0F | pdb_00009p0f

Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb9P0F/pdb

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


• Deposited: 2025-06-06 Released: 2025-06-25 
• Deposition Author(s): Minasov, G., Shuvalova, L., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)
• 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: 2.35 Å
• R-Value Free: 
  0.259 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2

Minasov, G., Shuvalova, L., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.26 kDa 
• Atom Count: 2,244 
• Modeled Residue Count: 276 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 4	A, B, C	92	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	D [auth A], E [auth A], F [auth B], G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.259 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.691	α = 90
b = 125.541	β = 90
c = 89.862	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Minasov, G., Shuvalova, L., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00035

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release