8WRX | pdb_00008wrx

Anti-CRISPR type II-A 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.221 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain.

Kim, G.E.Park, H.H.

(2024) Nucleic Acids Res 52: 6459-6471

  • DOI: https://doi.org/10.1093/nar/gkae357
  • Primary Citation Related Structures: 
    8WRX

  • PubMed Abstract: 

    CRISPR-Cas systems serve as adaptive immune systems in bacteria and archaea, protecting against phages and other mobile genetic elements. However, phages and archaeal viruses have developed countermeasures, employing anti-CRISPR (Acr) proteins to counteract CRISPR-Cas systems. Despite the revolutionary impact of CRISPR-Cas systems on genome editing, concerns persist regarding potential off-target effects. Therefore, understanding the structural and molecular intricacies of diverse Acrs is crucial for elucidating the fundamental mechanisms governing CRISPR-Cas regulation. In this study, we present the structure of AcrIIA28 from Streptococcus phage Javan 128 and analyze its structural and functional features to comprehend the mechanisms involved in its inhibition of Cas9. Our current study reveals that AcrIIA28 is a metalloprotein that contains Zn2+ and abolishes the cleavage activity of Cas9 only from Streptococcus pyrogen (SpyCas9) by directly interacting with the REC3 domain of SpyCas9. Furthermore, we demonstrate that the AcrIIA28 interaction prevents the target DNA from being loaded onto Cas9. These findings indicate the molecular mechanisms underlying AcrIIA28-mediated Cas9 inhibition and provide valuable insights into the ongoing evolutionary battle between bacteria and phages.


  • Organizational Affiliation
    • College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 10.62 kDa 
  • Atom Count: 821 
  • Modeled Residue Count: 86 
  • Deposited Residue Count: 88 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-CRISPR protein AcrIIA2888Streptococcus phage Javan128Mutation(s): 0 
UniProt
Find proteins for A0ACD6BAA1 (Streptococcus phage Javan128)
Explore A0ACD6BAA1 
Go to UniProtKB:  A0ACD6BAA1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6BAA1
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.221 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.43α = 90
b = 64.43β = 90
c = 62.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxDCdata collection
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release