5Y6A

Crystal structure of the anti-CRISPR protein, AcrIIA1

• PDB DOI: https://doi.org/10.2210/pdb5Y6A/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Listeria monocytogenes J0161
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-11 Released: 2017-11-29 
• Deposition Author(s): Ka, D., An, S.Y., Suh, J.Y., Bae, E.
• Funding Organization(s): Rural Development Administration, the Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Crystal structure of an anti-CRISPR protein, AcrIIA1

Ka, D., An, S.Y., Suh, J.Y., Bae, E.

(2018) Nucleic Acids Res 46: 485-492

• PubMed: 29182776 
• DOI: https://doi.org/10.1093/nar/gkx1181
• Primary Citation of Related Structures:  
  5Y69, 5Y6A


• PubMed Abstract: 
  

  Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide bacteria with RNA-based adaptive immunity against phage infection. To counteract this defense mechanism, phages evolved anti-CRISPR (Acr) proteins that inactivate the CRISPR-Cas systems. AcrIIA1, encoded by Listeria monocytogenes prophages, is the most prevalent among the Acr proteins targeting type II-A CRISPR-Cas systems and has been used as a marker to identify other Acr proteins. Here, we report the crystal structure of AcrIIA1 and its RNA-binding affinity. AcrIIA1 forms a dimer with a novel two helical-domain architecture. The N-terminal domain of AcrIIA1 exhibits a helix-turn-helix motif similar to transcriptional factors. When overexpressed in Escherichia coli, AcrIIA1 associates with RNAs, suggesting that AcrIIA1 functions via nucleic acid recognition. Taken together, the unique structural and functional features of AcrIIA1 suggest its distinct mode of Acr activity, expanding the diversity of the inhibitory mechanisms employed by Acr proteins.

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Organizational Affiliation: 

Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.

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: 34.94 kDa 
• Atom Count: 2,526 
• Modelled Residue Count: 292 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chain A and B	A, B	151	Listeria monocytogenes J0161	Mutation(s): 0  Gene Names: LMOG_03146
UniProt
Find proteins for A8ATW7 (Listeria phage A006) Explore A8ATW7  Go to UniProtKB:  A8ATW7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.435	α = 90
b = 55.42	β = 96.01
c = 46.504	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
PHENIX	phasing
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Ka, D., An, S.Y., Suh, J.Y., Bae, E.

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Funding Organization	Location	Grant Number
Rural Development Administration	Korea, Republic Of	PJ01111201
the Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology	Korea, Republic Of	NRF-2016R1D1A1A09916821

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description