9R8S | pdb_00009r8s

A viral SAVED protein with ring nuclease activity subverts type III CRISPR defence

• PDB DOI: https://doi.org/10.2210/pdb9R8S/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Thermocrinis Great Boiling Spring virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-16 Released: 2025-07-02 
• Deposition Author(s): McMahon, S.A., White, M.F., Orzechowski, M., Hoikkala, V., Chi, H., Gloster, T.M.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.207 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.178 (DCC) 

Starting Model: in silico

Literature

A viral SAVED protein with ring nuclease activity degrades the CRISPR second messenger cA4

Orzechowski, M., Hoikkala, V., Chi, H., McMahon, S.A., Gloster, T.M., White, M.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 55.45 kDa 
• Atom Count: 4,025 
• Modeled Residue Count: 473 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SMODS-associated and fused to various effectors domain-containing protein	A, B	243	Thermocrinis Great Boiling Spring virus	Mutation(s): 0
UniProt
Find proteins for A0A823AEM5 (Thermocrinis Great Boiling Spring virus) Explore A0A823AEM5  Go to UniProtKB:  A0A823AEM5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.207 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.178 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.614	α = 90
b = 110.614	β = 90
c = 113.027	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): McMahon, S.A., White, M.F., Orzechowski, M., Hoikkala, V., Chi, H., Gloster, T.M.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101018608

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release