9KJ9 | pdb_00009kj9

Anti-CRISPR protein AcrVIA6

• PDB DOI: https://doi.org/10.2210/pdb9KJ9/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Rhodobacter capsulatus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-12 Released: 2025-07-02 
• Deposition Author(s): Han, J.H., Park, H.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: in silico

Literature

AcrVIA6 Is a Monomeric DNA-Binding Protein That Does Not Directly Inhibit Cas13a.

Han, J.H., Lee, S.Y., Park, H.H.

(2025) FASEB J 39: e70753-e70753

• PubMed: 40540289 
• DOI: https://doi.org/10.1096/fj.202500684R
• Primary Citation of Related Structures:  
  9KJ9


• PubMed Abstract: 
  

  The CRISPR-Cas system is a crucial adaptive immune mechanism in prokaryotes, providing defense against invading genetic elements. Among various CRISPR-Cas systems, the type VI-A system, employing RNA-guided RNase Cas13a, has been extensively studied for its ability to target and degrade single-stranded RNA. Anti-CRISPR (Acr) proteins have evolved as natural inhibitors of these systems, with AcrVIA proteins specifically targeting the Cas13a enzyme. However, there is currently conflicting debate regarding the anti-CRISPR function of AcrVIA6. This study reveals that AcrVIA6 functions as a DNA-binding protein rather than a Cas13a inhibitor, as it does not block RNA cleavage. These findings challenge its role in CRISPR-Cas regulation.

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 10.6 kDa 
• Atom Count: 686 
• Modeled Residue Count: 85 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-CRISPR protein	A	93	Rhodobacter capsulatus	Mutation(s): 0  Gene Names: RCAP_rcc02927
UniProt
Find proteins for D5APT5 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)) Explore D5APT5  Go to UniProtKB:  D5APT5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.68	α = 90
b = 85.55	β = 90
c = 43.85	γ = 90

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: 2025-07-02 
Deposition Author(s): Han, J.H., Park, H.H.

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

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release