7VJQ

Pectobacterium phage ZF40 apo-aca2 complexed with 26bp DNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2.

Liu, Y.Zhang, L.Guo, M.Chen, L.Wu, B.Huang, H.

(2021) J Biol Chem 297: 101357-101357

  • DOI: https://doi.org/10.1016/j.jbc.2021.101357
  • Primary Citation of Related Structures:  
    7FA3, 7VJM, 7VJN, 7VJO, 7VJP, 7VJQ

  • PubMed Abstract: 

    It has been shown that phages have evolved anti-CRISPR (Acr) proteins to inhibit host CRISPR-Cas systems. Most acr genes are located upstream of anti-CRISPR-associated (aca) genes, which is instrumental for identifying these acr genes. Thus far, eight Aca families (Aca1-Aca8) have been identified, all proteins of which share low sequence homology and bind to different target DNA sequences. Recently, Aca1 and Aca2 proteins were discovered to function as repressors by binding to acr-aca promoters, thus implying a potential anti-anti-CRISPR mechanism. However, the structural basis for the repression roles of Aca proteins is still unknown. Here, we elucidated apo-structures of Aca1 and Aca2 proteins and their complex structures with their cognate operator DNA in two model systems, the Pseudomonas phage JBD30 and the Pectobacterium carotovorum template phage ZF40. In combination with biochemical and cellular assays, our study unveils dimerization and DNA-recognition mechanisms of Aca1 and Aca2 family proteins, thus revealing the molecular basis for Aca1-and Aca2-mediated anti-CRISPR repression. Our results also shed light on understanding the repression roles of other Aca family proteins and autoregulation roles of acr-aca operons.


  • Organizational Affiliation

    School of Life Science and Technology, Harbin Institute of Technology, Harbin, China; Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-CRISPR-associated protein Aca2
A, B
121Pectobacterium phage ZF40Mutation(s): 0 
Gene Names: ZF40_0030
UniProt
Find proteins for H9C180 (Pectobacterium phage ZF40)
Explore H9C180 
Go to UniProtKB:  H9C180
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9C180
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (27-MER)27synthetic construct
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (27-MER)27synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
K [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.31α = 90
b = 168.473β = 90.06
c = 41.492γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description