6EYX | pdb_00006eyx

Anti-CRISPR AcrIIa6 tetragonal form

• PDB DOI: https://doi.org/10.2210/pdb6EYX/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Moineauvirus DT1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-13 Released: 2018-06-06 
• Deposition Author(s): Cambillau, C., Amigues, B., Moineau, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins.

Hynes, A.P., Rousseau, G.M., Agudelo, D., Goulet, A., Amigues, B., Loehr, J., Romero, D.A., Fremaux, C., Horvath, P., Doyon, Y., Cambillau, C., Moineau, S.

(2018) Nat Commun 9: 2919-2919

• PubMed: 30046034 
• DOI: https://doi.org/10.1038/s41467-018-05092-w
• Primary Citation Related Structures: 
  6EYX, 6EYY


• PubMed Abstract: 
  

  CRISPR-Cas systems are bacterial anti-viral systems, and bacterial viruses (bacteriophages, phages) can carry anti-CRISPR (Acr) proteins to evade that immunity. Acrs can also fine-tune the activity of CRISPR-based genome-editing tools. While Acrs are prevalent in phages capable of lying dormant in a CRISPR-carrying host, their orthologs have been observed only infrequently in virulent phages. Here we identify AcrIIA6, an Acr encoded in 33% of virulent Streptococcus thermophilus phage genomes. The X-ray structure of AcrIIA6 displays some features unique to this Acr family. We compare the activity of AcrIIA6 to those of other Acrs, including AcrIIA5 (also from S. thermophilus phages), and characterize their effectiveness against a range of CRISPR-Cas systems. Finally, we demonstrate that both Acr families from S. thermophilus phages inhibit Cas9-mediated genome editing of human cells.

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Organizational Affiliation: 
• Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.
Farncombe Family Digestive Health Research Institute, McMaster University. Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.
Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada.
Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France.
Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France.
DuPont Nutrition and Health, 3329 Agriculture Dr, Madison, WI, 53716, USA.
DuPont Nutrition and Health, BP 10, 86220, Dangé-Saint-Romain, France.
Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. [e-mail].
Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. [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

Macromolecule Content 

• Total Structure Weight: 43.41 kDa 
• Atom Count: 3,306 
• Modeled Residue Count: 360 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AcrIIa6	A, B	185	Moineauvirus DT1	Mutation(s): 0
UniProt
Find proteins for Q9XJC1 (Streptococcus phage DT1) Explore Q9XJC1  Go to UniProtKB:  Q9XJC1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.37	α = 90
b = 71.37	β = 90
c = 177.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Cambillau, C., Amigues, B., Moineau, S.

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2018-08-08
  Changes: Data collection, Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references