3EW5

Structure of the tetragonal crystal form of X (ADRP) domain from FCoV

• PDB DOI: https://doi.org/10.2210/pdb3EW5/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Feline infectious peritonitis virus (strain 79-1146)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-14 Released: 2009-10-27 
• Deposition Author(s): Wojdyla, J.A., Manolaridis, I., Tucker, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Structure of the X (ADRP) domain of nsp3 from feline coronavirus

Wojdyla, J.A., Manolaridis, I., Snijder, E.J., Gorbalenya, A.E., Coutard, B., Piotrowski, Y., Hilgenfeld, R., Tucker, P.A.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1292-1300

• PubMed: 19966415 
• DOI: https://doi.org/10.1107/S0907444909040074
• Primary Citation of Related Structures:  
  3ETI, 3EW5, 3JZT


• PubMed Abstract: 
  

  The structure of the X (or ADRP) domain of a pathogenic variant of feline coronavirus (FCoV) has been determined in tetragonal and cubic crystal forms to 3.1 and 2.2 A resolution, respectively. In the tetragonal crystal form, glycerol-3-phosphate was observed in the ADP-ribose-binding site. Both crystal forms contained large solvent channels and had a solvent content of higher than 70%. Only very weak binding of this domain to ADP-ribose was detected in vitro. However, the structure with ADP-ribose bound was determined in the cubic crystal form at 3.9 A resolution. The structure of the FCoV X domain had the expected macro-domain fold and is the first structure of this domain from a coronavirus belonging to subgroup 1a.

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Organizational Affiliation: 

EMBL Hamburg Outstation, c/o DESY, D-22603 Hamburg, Germany.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.55 kDa 
• Atom Count: 4,030 
• Modelled Residue Count: 502 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
macro domain of Non-structural protein 3	A, B, C	168	Feline infectious peritonitis virus (strain 79-1146)	Mutation(s): 0
UniProt
Find proteins for Q98VG9 (Feline coronavirus (strain FIPV WSU-79/1146)) Explore Q98VG9  Go to UniProtKB:  Q98VG9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1GP	F [auth A], K [auth B], P [auth C]	SN-GLYCEROL-1-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-VKHMYHEASA-N
SO4	E [auth A], G [auth A], H [auth B], L [auth C], M [auth C], O [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], I [auth B], J [auth B], N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.13	α = 90
b = 161.13	β = 90
c = 98.29	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Wojdyla, J.A., Manolaridis, I., Tucker, P.A.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations