6ARZ | pdb_00006arz

Structure of a phage anti-CRISPR protein

• PDB DOI: https://doi.org/10.2210/pdb6ARZ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Pseudomonas phage JBD5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-23 Released: 2018-08-29 
• Deposition Author(s): Calmettes, C., Shah, M., Pawluk, A., Davidson, A.R., Maxwell, K.L., Moraes, T.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.221 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Disabling a Type I-E CRISPR-Cas Nuclease with a Bacteriophage-Encoded Anti-CRISPR Protein.

Pawluk, A., Shah, M., Mejdani, M., Calmettes, C., Moraes, T.F., Davidson, A.R., Maxwell, K.L.

(2017) mBio 8

• PubMed: 29233895 
• DOI: https://doi.org/10.1128/mBio.01751-17
• Primary Citation Related Structures: 
  6ARZ, 6AS3, 6AS4


• PubMed Abstract: 
  

  CRISPR (clustered regularly interspaced short palindromic repeat)-Cas adaptive immune systems are prevalent defense mechanisms in bacteria and archaea. They provide sequence-specific detection and neutralization of foreign nucleic acids such as bacteriophages and plasmids. One mechanism by which phages and other mobile genetic elements are able to overcome the CRISPR-Cas system is through the expression of anti-CRISPR proteins. Over 20 different families of anti-CRISPR proteins have been described, each of which inhibits a particular type of CRISPR-Cas system. In this work, we determined the structure of type I-E anti-CRISPR protein AcrE1 by X-ray crystallography. We show that AcrE1 binds to the CRISPR-associated helicase/nuclease Cas3 and that the C-terminal region of the anti-CRISPR protein is important for its inhibitory activity. We further show that AcrE1 can convert the endogenous type I-E CRISPR system into a programmable transcriptional repressor. IMPORTANCE The CRISPR-Cas immune system provides bacteria with resistance to invasion by potentially harmful viruses, plasmids, and other foreign mobile genetic elements. This study presents the first structural and mechanistic insight into a phage-encoded protein that inactivates the type I-E CRISPR-Cas system in Pseudomonas aeruginosa The interaction of this anti-CRISPR protein with the CRISPR-associated helicase/nuclease proteins Cas3 shuts down the CRISPR-Cas system and protects phages carrying this gene from destruction. This interaction also allows the repurposing of the endogenous type I-E CRISPR system into a programmable transcriptional repressor, providing a new biotechnological tool for genetic studies of bacteria encoding this type I-E CRISPR-Cas system.

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Organizational Affiliation: 
• Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada [e-mail] [e-mail].
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.15 kDa 
• Atom Count: 2,358 
• Modeled Residue Count: 282 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C	108	Pseudomonas phage JBD5	Mutation(s): 0  Gene Names: JBD5_034
UniProt
Find proteins for L7P7L6 (Pseudomonas phage JBD5) Explore L7P7L6  Go to UniProtKB:  L7P7L6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR	G [auth B], H [auth B], I [auth B], J [auth B], K [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.221 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.137	α = 90
b = 63.959	β = 100.94
c = 59.701	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Calmettes, C., Shah, M., Pawluk, A., Davidson, A.R., Maxwell, K.L., Moraes, T.F.

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Funding Organization	Location	Grant Number
	Canada	--

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Refinement description, Structure summary