8V44

N-terminal truncation of CRISPR-associated DinG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.231 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The N-terminal domain of Type IV-A1 CRISPR-associated DinG is vulnerable to proteolysis.

Hallmark, T.Williams, A.A.Redman, O.Guinn, B.Judd, C.Jackson, R.N.

(2024) MicroPubl Biol 2024

  • DOI: https://doi.org/10.17912/micropub.biology.001226
  • Primary Citation of Related Structures:  
    8V44

  • PubMed Abstract: 

    CasDinG is an ATP-dependent 5'-3' DNA helicase essential for bacterial Type IV-A1 CRISPR associated immunity. CasDinG contains an essential N-terminal domain predicted to bind DNA. To better understand the role of the N-terminal domain, we attempted to co-crystallize CasDinG with DNA substrates. We successfully crystallized CasDinG in a tightly packed, crystal conformation with previously unobserved unit cell dimensions. However, the structure lacked electron density for a bound DNA substrate and the CasDinG N-terminal domain. Additionally, the tight crystal packing disallowed space for the N-terminal domain, indicating that the N-terminal domain was proteolyzed before crystallization. Follow up experiments revealed that the N-terminal domain of CasDinG is proteolyzed after a few days at room temperature, but is protected from proteolysis at 4°C. These data provide a distinct x-ray crystal structure of CasDinG and indicate the essential N-terminal domain of CasDinG is prone to proteolysis.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CasDinG726Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0AA82WPF0 (Pseudomonas aeruginosa)
Explore A0AA82WPF0 
Go to UniProtKB:  A0AA82WPF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA82WPF0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.04α = 90
b = 84.01β = 90
c = 97.619γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM138080

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Refinement description
  • Version 1.2: 2024-07-31
    Changes: Database references