8JFR

N-terminal domain of AcrIIA15 in complex with palindromic DNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An anti-CRISPR that represses its own transcription while blocking Cas9-target DNA binding.

Deng, X.Sun, W.Li, X.Wang, J.Cheng, Z.Sheng, G.Wang, Y.

(2024) Nat Commun 15: 1806-1806

  • DOI: https://doi.org/10.1038/s41467-024-45987-5
  • Primary Citation of Related Structures:  
    8JFO, 8JFR, 8JFT, 8JFU, 8JG9

  • PubMed Abstract: 

    AcrIIA15 is an anti-CRISPR (Acr) protein that inhibits Staphylococcus aureus Cas9 (SaCas9). Although previous studies suggested it has dual functions, the structural and biochemical basis for its two activities remains unclear. Here, we determined the cryo-EM structure of AcrIIA15 in complex with SaCas9-sgRNA to reveal the inhibitory mechanism of the Acr's C-terminal domain (CTD) in mimicking dsDNA to block protospacer adjacent motif (PAM) recognition. For the N-terminal domain (NTD), our crystal structures of the AcrIIA15-promoter DNA show that AcrIIA15 dimerizes through its NTD to recognize double-stranded (ds) DNA. Further, AcrIIA15 can simultaneously bind to both SaCas9-sgRNA and promoter DNA, creating a supercomplex of two Cas9s bound to two CTDs converging on a dimer of the NTD bound to a dsDNA. These findings shed light on AcrIIA15's inhibitory mechanisms and its autoregulation of transcription, enhancing our understanding of phage-host interactions and CRISPR defense.


  • Organizational Affiliation

    Key Laboratory of RNA Science and Engineering, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AcrIIA15A [auth B],
B [auth D],
E [auth A],
F [auth C]
63Staphylococcus delphiniMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*TP*AP*TP*GP*AP*CP*AP*AP*AP*TP*GP*TP*CP*AP*TP*AP*G)-3')C [auth E],
G
19Staphylococcus delphini
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*TP*AP*TP*GP*AP*CP*AP*TP*TP*TP*GP*TP*CP*AP*TP*AP*A)-3')D [auth F],
H
19Staphylococcus delphini
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.712α = 90
b = 58.712β = 90
c = 240.593γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31930065
National Natural Science Foundation of China (NSFC)China31725008

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references, Refinement description