6VYO

Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2

• PDB DOI:  https://doi.org/10.2210/pdb6VYO/pdb

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


• Deposited: 2020-02-27 Released: 2020-03-11 
• Deposition Author(s): Chang, C., Michalska, K., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Kim, Y., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 

Literature

Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2

Chang, C., Michalska, K., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Kim, Y., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 57.67 kDa 
• Atom Count: 4,683 
• Modelled Residue Count: 499 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D	128	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: N
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	E [auth A], G [auth A], L [auth B], Q [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	K [auth B], P [auth C], S [auth D], T [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	H [auth A], J [auth A], M [auth B], R [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], I [auth A], N [auth C], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m36vyo

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.238	α = 90
b = 77.43	β = 90
c = 114.039	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
SBC-Collect	data collection

Structure Validation

Currently 6VYO does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): Chang, C., Michalska, K., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Kim, Y., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Structure summary
• Version 2.0: 2020-04-08
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
• Version 3.0: 2020-05-06
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 3.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary