6XB4 | pdb_00006xb4

Structure of PrGV poxin in post-reactive state with Gp[2'-5']Ap[3']

PDB DOI: https://doi.org/10.2210/pdb6XB4/pdb

Classification: HYDROLASE
Organism(s): Pieris rapae granulovirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-06-05 Released: 2020-11-25
Deposition Author(s): Eaglesham, J.B., McCarty, K.L., Kranzusch, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.207 (Depositor), 0.214 (DCC)
R-Value Work:
0.183 (Depositor)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host-pathogen conflict.

Eaglesham, J.B., McCarty, K.L., Kranzusch, P.J.

(2020) Elife 9

PubMed: 33191912 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.59753
Primary Citation Related Structures:
6XB3, 6XB4, 6XB5, 6XB6

PubMed Abstract:
DNA viruses in the family Poxviridae encode poxin enzymes that degrade the immune second messenger 2'3'-cGAMP to inhibit cGAS-STING immunity in mammalian cells. The closest homologs of poxin exist in the genomes of insect viruses suggesting a key mechanism of cGAS-STING evasion may have evolved outside of mammalian biology. Here we use a biochemical and structural approach to discover a broad family of 369 poxins encoded in diverse viral and animal genomes and define a prominent role for 2'3'-cGAMP cleavage in metazoan host-pathogen conflict. Structures of insect poxins reveal unexpected homology to flavivirus proteases and enable identification of functional self-cleaving poxins in RNA-virus polyproteins. Our data suggest widespread 2'3'-cGAMP signaling in insect antiviral immunity and explain how a family of cGAS-STING evasion enzymes evolved from viral proteases through gain of secondary nuclease activity. Poxin acquisition by poxviruses demonstrates the importance of environmental connections in shaping evolution of mammalian pathogens.

Organizational Affiliation

Department of Microbiology, Harvard Medical School, Boston, United States.

Macromolecule Content

Total Structure Weight: 94.21 kDa
Atom Count: 7,103
Modeled Residue Count: 765
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poxin	A, B, C, D	200	Pieris rapae granulovirus	Mutation(s): 0
UniProt
Find proteins for A0ACD6B8Q5 (Pieris rapae granulovirus) Explore A0ACD6B8Q5 Go to UniProtKB: A0ACD6B8Q5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8Q5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9BG (Subject of Investigation/LOI) Query on 9BG Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth C] SDF format, chain E [auth B] MOL2 format, chain G [auth D] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] mmCIF format, chain G [auth D] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B]	E [auth B], F [auth C], G [auth D]	2',5'-GpAp C₂₀ H₂₆ N₁₀ O₁₄ P₂ OVXKSNAROFCXFB-INFSMZHSSA-N		Interactions Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.207 (Depositor), 0.214 (DCC)
R-Value Work: 0.183 (Depositor)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.47	α = 90
b = 58.14	β = 108.548
c = 100.698	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

Eaglesham, J.B.

Kranzusch, P.J.

Revision History (Full details and data files)

Version 1.0: 2020-11-25
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.