7VBD | pdb_00007vbd

Crystal structure of SARS-Cov-2 nucleocapsid N-terminal domain (NTD) protein,pH8.0

• PDB DOI: https://doi.org/10.2210/pdb7VBD/pdb

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


• Deposited: 2021-08-31 Released: 2022-08-31 
• Deposition Author(s): Zeng, P., Zhou, X.L., Zhong, F.L., Li, J., Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-Cov-2 nucleocapsid N-terminal domain (NTD) protein,pH8.0

Zeng, P., Zhou, X.L., Zhong, F.L., Li, J., Zhang, J.

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: 55.95 kDa 
• Atom Count: 3,827 
• Modeled Residue Count: 471 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D	127	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.977	α = 90
b = 55.133	β = 95.058
c = 84.293	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Zeng, P., Zhou, X.L., Zhong, F.L., Li, J., Zhang, J.

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description