7C22 | pdb_00007c22

Crystal structure of the C-terminal domain of SARS-CoV-2 nucleocapsid protein

• PDB DOI: https://doi.org/10.2210/pdb7C22/pdb

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


• Deposited: 2020-05-07 Released: 2020-05-20 
• Deposition Author(s): Zhou, R.J., Zeng, R., Lei, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of the C-terminal domain of SARS-CoV-2 nucleocapsid protein.

Zhou, R., Zeng, R., von Brunn, A., Lei, J.

(2020) Mol Biomed 1: 2-2

• DOI: https://doi.org/10.1186/s43556-020-00001-4

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.72 kDa 
• Atom Count: 3,978 
• Modeled Residue Count: 442 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D	120	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)	E [auth A], G [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.763	α = 106.79
b = 49.458	β = 90.05
c = 68.819	γ = 97.79

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Zhou, R.J., Zeng, R., Lei, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2020YFS0010/HX2019nCoV039

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-08-12
  Changes: Database references
• Version 1.2: 2020-10-28
  Changes: Database references
• Version 1.3: 2021-03-10
  Changes: Structure summary
• Version 1.4: 2022-02-16
  Changes: Database references
• Version 1.5: 2023-11-29
  Changes: Data collection, Refinement description