1LUZ

Crystal Structure of the K3L Protein From Vaccinia Virus (Wisconsin Strain)

• PDB DOI: https://doi.org/10.2210/pdb1LUZ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Vaccinia virus WR
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2002-05-23 Released: 2002-08-28 
• Deposition Author(s): Dar, A.C., Sicheri, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.256 (Depositor) 
• R-Value Work: 
  0.232 (Depositor) 

Literature

X-ray crystal structure and functional analysis of vaccinia virus K3L reveals molecular determinants for PKR subversion and substrate recognition.

Dar, A.C., Sicheri, F.

(2002) Mol Cell 10: 295-305

• PubMed: 12191475 
• DOI: https://doi.org/10.1016/s1097-2765(02)00590-7
• Primary Citation of Related Structures:  
  1LUZ


• PubMed Abstract: 
  

  The vaccinia virus protein K3L subverts the mammalian antiviral defense mechanism by inhibiting the RNA-dependent protein kinase PKR. K3L is a structural mimic of PKR's natural substrate, the translation initiation factor eIF2alpha. To further our understanding of K3L inhibitory function and PKR substrate recognition, we have solved the 1.8 A X-ray crystal structure of K3L. The structure consists of a five-strand beta barrel with an intervening helix insert region similar in topology to the functionally divergent S1 domain. Mutational analysis identifies two proximal regions of the K3L structure as possessing specialized PKR binding and inhibitory function. Further analysis reveals that PKR dimerization composes a key switch that regulates both its catalytic activation and its molecular recognition of K3L and eIF2alpha.

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Organizational Affiliation: 

Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.43 kDa 
• Atom Count: 1,491 
• Modelled Residue Count: 168 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein K3	A, B	88	Vaccinia virus WR	Mutation(s): 3  Gene Names: K3L
UniProt
Find proteins for P18378 (Vaccinia virus (strain Western Reserve)) Explore P18378  Go to UniProtKB:  P18378

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.256 (Depositor) 
• R-Value Work:  0.232 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.119	α = 90
b = 49.58	β = 100.69
c = 59.938	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-28 
Deposition Author(s): Dar, A.C., Sicheri, F.

Revision History  

• Version 1.0: 2002-08-28
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary