7TAX

Cryo-EM structure of the Csy-AcrIF24-promoter DNA complex

  • Classification: HYDROLASE/RNA/DNA
  • Organism(s): Pseudomonas
  • Expression System: Escherichia
  • Mutation(s): No 

  • Deposited: 2021-12-21 Released: 2022-09-21 
  • Deposition Author(s): Mukherjee, I.A., Chang, L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor.

Mukherjee, I.A.Gabel, C.Noinaj, N.Bondy-Denomy, J.Chang, L.

(2022) Nat Chem Biol 18: 1417-1424

  • DOI: https://doi.org/10.1038/s41589-022-01137-w
  • Primary Citation of Related Structures:  
    7T3J, 7T3K, 7T3L, 7TAW, 7TAX

  • PubMed Abstract: 

    Anti-CRISPR (Acr) proteins are encoded by phages to inactivate CRISPR-Cas systems of bacteria and archaea and are used to enhance the CRISPR toolbox for genome editing. Here we report the structure and mechanism of AcrIF24, an Acr protein that inhibits the type I-F CRISPR-Cas system from Pseudomonas aeruginosa. AcrIF24 is a homodimer that associates with two copies of the surveillance complex (Csy) and prevents the hybridization between CRISPR RNA and target DNA. Furthermore, AcrIF24 functions as an anti-CRISPR-associated (Aca) protein to repress the transcription of the acrIF23-acrIF24 operon. Alone or in complex with Csy, AcrIF24 is capable of binding to the acrIF23-acrIF24 promoter DNA with nanomolar affinity. The structure of a Csy-AcrIF24-promoter DNA complex at 2.7 Å reveals the mechanism for transcriptional suppression. Our results reveal that AcrIF24 functions as an Acr-Aca fusion protein, and they extend understanding of the diverse mechanisms used by Acr proteins.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein Csy1434PseudomonasMutation(s): 0 
Gene Names: csy1PA14_33330
UniProt
Find proteins for Q02ML9 (Pseudomonas aeruginosa (strain UCBPP-PA14))
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Go to UniProtKB:  Q02ML9
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UniProt GroupQ02ML9
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR type I-F/YPEST-associated protein Csy2327PseudomonasMutation(s): 0 
Gene Names: csy2ALP65_00953IPC1598_32520IPC29_26970PA52Ts2_3638PACL_0128
UniProt
Find proteins for Q02MM0 (Pseudomonas aeruginosa (strain UCBPP-PA14))
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Go to UniProtKB:  Q02MM0
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UniProt GroupQ02MM0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas6/Csy4187PseudomonasMutation(s): 0 
Gene Names: cas6fcsy4PA14_33300
EC: 3.1
UniProt
Find proteins for Q02MM2 (Pseudomonas aeruginosa (strain UCBPP-PA14))
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UniProt GroupQ02MM2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR type I-F/YPEST-associated protein Csy3
D, E, F, G, H
D, E, F, G, H, I
360PseudomonasMutation(s): 0 
Gene Names: PA52Ts2_3639
UniProt
Find proteins for Q02MM1 (Pseudomonas aeruginosa (strain UCBPP-PA14))
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UniProt GroupQ02MM1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
AcrIF24
J, K
228PseudomonasMutation(s): 0 
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (61-MER)L [auth M]61Pseudomonas
Sequence Annotations
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*TP*AP*GP*CP*TP*CP*GP*AP*TP*TP*CP*GP*AP*GP*CP*TP*AP*A)-3')M [auth Y]19Pseudomonas
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*AP*GP*CP*TP*CP*GP*AP*AP*TP*CP*GP*AP*GP*CP*TP*AP*T)-3')N [auth X]19Pseudomonas
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM138675

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2022-12-07
    Changes: Database references, Refinement description
  • Version 1.3: 2024-06-05
    Changes: Data collection, Refinement description