9KJB | pdb_00009kjb

Crystal structure of Anti-CRISPR AcrIE7

• PDB DOI: https://doi.org/10.2210/pdb9KJB/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-12 Released: 2025-04-16 
• Deposition Author(s): Kim, D.Y., Park, H.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: in silico

Literature

AcrIE7 inhibits the CRISPR-Cas system by directly binding to the R-loop single-stranded DNA.

Kim, D.Y., Lee, S.Y., Ha, H.J., Park, H.H.

(2025) Proc Natl Acad Sci U S A 122: e2423205122-e2423205122

• PubMed: 40178896 
• DOI: https://doi.org/10.1073/pnas.2423205122
• Primary Citation of Related Structures:  
  9KJB


• PubMed Abstract: 
  

  The CRISPR-Cas system is a well-known adaptive immune system in bacteria, and a prominent mechanism for evading this immunity involves anti-CRISPR (Acr) proteins, which employ various methods to neutralize the CRISPR-Cas system. In this study, using structural and biochemical analyses, we revealed that AcrIE7 binds to the single-stranded DNA in the R-loop formed when Cascade encounters the target DNA, thereby preventing Cas3 from cleaving the DNA. This represents a different inhibition strategy distinct from previously reported Acr mechanisms and offers insights into CRISPR-Cas inhibition.

---

Organizational Affiliation: 
• Department of Global Innovative Drugs, College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 13.03 kDa 
• Atom Count: 932 
• Modeled Residue Count: 105 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AcrIE7	A	114	Pseudomonas aeruginosa	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.45	α = 90
b = 59.45	β = 90
c = 63.88	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Kim, D.Y., Park, H.H.

---

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release