6EA6 | pdb_00006ea6

Structure of VACV poxin 2'3' cGAMP-specific nuclease

• PDB DOI: https://doi.org/10.2210/pdb6EA6/pdb

• Classification: HYDROLASE
• Organism(s): Vaccinia virus WR
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-02 Released: 2019-02-06 
• Deposition Author(s): Eaglesham, J.B., Kranzusch, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Viral and metazoan poxins are cGAMP-specific nucleases that restrict cGAS-STING signalling.

Eaglesham, J.B., Pan, Y., Kupper, T.S., Kranzusch, P.J.

(2019) Nature 566: 259-263

• PubMed: 30728498 
• DOI: https://doi.org/10.1038/s41586-019-0928-6
• Primary Citation Related Structures: 
  6EA6, 6EA8, 6EA9


• PubMed Abstract: 
  

  Cytosolic DNA triggers innate immune responses through the activation of cyclic GMP-AMP synthase (cGAS) and production of the cyclic dinucleotide second messenger 2',3'-cyclic GMP-AMP (cGAMP) ^1-4 . 2',3'-cGAMP is a potent inducer of immune signalling; however, no intracellular nucleases are known to cleave 2',3'-cGAMP and prevent the activation of the receptor stimulator of interferon genes (STING) ^5-7 . Here we develop a biochemical screen to analyse 24 mammalian viruses, and identify poxvirus immune nucleases (poxins) as a family of 2',3'-cGAMP-degrading enzymes. Poxins cleave 2',3'-cGAMP to restrict STING-dependent signalling and deletion of the poxin gene (B2R) attenuates vaccinia virus replication in vivo. Crystal structures of vaccinia virus poxin in pre- and post-reactive states define the mechanism of selective 2',3'-cGAMP degradation through metal-independent cleavage of the 3'-5' bond, converting 2',3'-cGAMP into linear Gp[2'-5']Ap[3']. Poxins are conserved in mammalian poxviruses. In addition, we identify functional poxin homologues in the genomes of moths and butterflies and the baculoviruses that infect these insects. Baculovirus and insect host poxin homologues retain selective 2',3'-cGAMP degradation activity, suggesting an ancient role for poxins in cGAS-STING regulation. Our results define poxins as a family of 2',3'-cGAMP-specific nucleases and demonstrate a mechanism for how viruses evade innate immunity.

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Organizational Affiliation: 
• Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
Harvard PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA.
Department of Dermatology and Harvard Skin Disease Research Center, Brigham and Women's Hospital, Boston, Harvard Medical School, Boston, MA, USA.
Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA.
Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA. [e-mail].
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA. [e-mail].
Harvard PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA. [e-mail].
Parker Institute for Cancer Immunotherapy, Dana-Farber Cancer Institute, Boston, MA, USA. [e-mail].

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: 100.29 kDa 
• Atom Count: 6,910 
• Modeled Residue Count: 773 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein B2	A, B [auth C], C [auth B], D	220	Vaccinia virus WR	Mutation(s): 0  Gene Names: VACWR184, B2R EC: 3.1
UniProt
Find proteins for Q01225 (Vaccinia virus (strain Western Reserve)) Explore Q01225  Go to UniProtKB:  Q01225

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.026	α = 90
b = 93.194	β = 105.63
c = 94.133	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Eaglesham, J.B., Kranzusch, P.J.

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Database references
• Version 1.2: 2019-02-27
  Changes: Data collection, Database references
• Version 1.3: 2019-12-11
  Changes: Derived calculations
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Structure summary