4OSS

Crystal structure of the S505Q mutant of TAL effector dHax3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Revisiting the TALE repeat

Deng, D.Yan, C.Y.Wu, J.P.Pan, X.J.Yan, N.

(2014) Protein Cell 5: 297-306

  • DOI: https://doi.org/10.1007/s13238-014-0035-2
  • Primary Citation of Related Structures:  
    4OSH, 4OSI, 4OSJ, 4OSK, 4OSL, 4OSM, 4OSQ, 4OSR, 4OSS, 4OST, 4OSV, 4OSW, 4OSZ, 4OT0, 4OT3, 4OTO

  • PubMed Abstract: 

    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.


  • Organizational Affiliation

    State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hax3
A, B
499Xanthomonas campestris pv. armoraciaeMutation(s): 18 
Gene Names: hax3
UniProt
Find proteins for Q3ZD72 (Xanthomonas campestris pv. armoraciae)
Explore Q3ZD72 
Go to UniProtKB:  Q3ZD72
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3ZD72
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*GP*TP*CP*TP*CP*TP*CP*T)-3')C [auth G],
E [auth I]
17N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')D [auth H],
F [auth J]
17N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.083α = 90
b = 87.072β = 103
c = 87.95γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description