8JB9 | pdb_00008jb9

Solution structure of Anti-CRISPR protein AcrIIC5

• PDB DOI: https://doi.org/10.2210/pdb8JB9/pdb

• Classification: PROTEIN BINDING
• Organism(s): Simonsiella muelleri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-08 Released: 2024-05-08 
• Deposition Author(s): Hong, S.H., Park, C., An, S.Y., Suh, J.Y.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1800 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural variants of AcrIIC5 inhibit Cas9 via divergent binding interfaces.

Hong, S.H., An, S.Y., Park, C., Kim, Y., Kim, E.H., Kim, N.K., Suh, J.Y.

(2025) Structure 33: 517-527.e5

• PubMed: 39826547 
• DOI: https://doi.org/10.1016/j.str.2024.12.014
• Primary Citation Related Structures: 
  8JB9


• PubMed Abstract: 
  

  CRISPR-Cas is a bacterial defense system that employs RNA-guided endonucleases to destroy invading foreign nucleic acids. Bacteriophages produce anti-CRISPR (Acr) proteins to evade CRISPR-Cas defense during the infection. AcrIIC5, a type II-C Cas9 inhibitor, exhibits unusual variations in the local backbone fold between its orthologs. Here we investigated how the folding variations affect the inhibition of target Cas9 using AcrIIC5 orthologs. Structural comparison of free AcrIIC5 _Smu and AcrIIC5 _Nch confirmed that the folding variation correlated with characteristic indels in the helical region. Mutagenesis and biochemical assays combined with AlphaFold2 predictions identified key residues of AcrIIC5 orthologs important for Cas9 inhibition. Remarkably, AcrIIC5 orthologs employed divergent binding interfaces via folding variations to inhibit the Cas9 targets. Our study suggests that Acr proteins have evolved structural variants to diversify key interfaces for target Cas9, which could be beneficial for the adaptation of phages to evasive mutations on the Cas9 surface.

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Organizational Affiliation: 
• Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea.
Biopharmaceutical Research Center, Korea Basic Science Institute, Ochang 28119, South Korea.
Advanced Analysis Data Center, Korea Institute of Science and Technology, Seoul 02792, South Korea.
Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.31 kDa 
• Atom Count: 1,073 
• Modeled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II-C anti-CRISPR protein, AcrIIC5	A	130	Simonsiella muelleri	Mutation(s): 0  Gene Names: HMPREF9021_01755
UniProt
Find proteins for V9H5N5 (Simonsiella muelleri ATCC 29453) Explore V9H5N5  Go to UniProtKB:  V9H5N5

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1800 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Hong, S.H., Park, C., An, S.Y., Suh, J.Y.

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

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Database references, Structure summary