7BB5 | pdb_00007bb5

Crystal structure of anti-CRISPR protein AcrIF9

• PDB DOI: https://doi.org/10.2210/pdb7BB5/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Aggregatibacter actinomycetemcomitans serotype e str. SC1083
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-12-17 Released: 2021-11-24 
• Deposition Author(s): Tamulaitiene, G., Sinkunas, T., Kupcinskaite, E.
• Funding Organization(s): Research Council of Lithuania

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.223 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Disarming of type I-F CRISPR-Cas surveillance complex by anti-CRISPR proteins AcrIF6 and AcrIF9.

Kupcinskaite, E., Tutkus, M., Kopustas, A., Asmontas, S., Jankunec, M., Zaremba, M., Tamulaitiene, G., Sinkunas, T.

(2022) Sci Rep 12: 15548-15548

• PubMed: 36109551 
• DOI: https://doi.org/10.1038/s41598-022-19797-y
• Primary Citation Related Structures: 
  7BB5


• PubMed Abstract: 
  

  CRISPR-Cas systems are prokaryotic adaptive immune systems that protect against phages and other invading nucleic acids. The evolutionary arms race between prokaryotes and phages gave rise to phage anti-CRISPR (Acr) proteins that act as a counter defence against CRISPR-Cas systems by inhibiting the effector complex. Here, we used a combination of bulk biochemical experiments, X-ray crystallography and single-molecule techniques to explore the inhibitory activity of AcrIF6 and AcrIF9 proteins against the type I-F CRISPR-Cas system from Aggregatibacter actinomycetemcomitans (Aa). We showed that AcrIF6 and AcrIF9 proteins hinder Aa-Cascade complex binding to target DNA. We solved a crystal structure of Aa1-AcrIF9 protein, which differ from other known AcrIF9 proteins by an additional structurally important loop presumably involved in the interaction with Cascade. We revealed that AcrIF9 association with Aa-Cascade promotes its binding to off-target DNA sites, which facilitates inhibition of CRISPR-Cas protection.

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Organizational Affiliation: 
• Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, 10257, Vilnius, Lithuania.
Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Savanoriu 231, 02300, Vilnius, Lithuania.
Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, 10257, Vilnius, Lithuania.
Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, 10257, Vilnius, Lithuania. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 10.33 kDa 
• Atom Count: 666 
• Modeled Residue Count: 76 
• Deposited Residue Count: 91 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AcrIF9	A	91	Aggregatibacter actinomycetemcomitans serotype e str. SC1083	Mutation(s): 0  Gene Names: SC1083_0445
UniProt
Find proteins for G4A6K5 (Aggregatibacter actinomycetemcomitans serotype e str. SC1083) Explore G4A6K5  Go to UniProtKB:  G4A6K5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.223 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.285	α = 90
b = 77.285	β = 90
c = 75.663	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Tamulaitiene, G., Sinkunas, T., Kupcinskaite, E.

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Funding Organization	Location	Grant Number
Research Council of Lithuania	Lithuania	S-MIP-17-47

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2022-12-07
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Refinement description