4GG4

Crystal structure of the TAL effector dHax3 bound to specific DNA-RNA hybrid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Specific DNA-RNA hybrid recognition by TAL effectors

Yin, P.Deng, D.Yan, C.Pan, X.J.Xi, J.J.Yan, N.Shi, Y.

(2012) Cell Rep 2: 707-713

  • DOI: 10.1016/j.celrep.2012.09.001

  • PubMed Abstract: 
  • The transcription activator-like (TAL) effector targets specific host promoter through its central DNA-binding domain, which comprises multiple tandem repeats (TALE repeats). Recent structural analyses revealed that the TALE repeats form a superhelic ...

    The transcription activator-like (TAL) effector targets specific host promoter through its central DNA-binding domain, which comprises multiple tandem repeats (TALE repeats). Recent structural analyses revealed that the TALE repeats form a superhelical structure that tracks along the forward strand of the DNA duplex. Here, we demonstrate that TALE repeats specifically recognize a DNA-RNA hybrid where the DNA strand determines the binding specificity. The crystal structure of a designed TALE in complex with the DNA-RNA hybrid was determined at a resolution of 2.5 Å. Although TALE repeats are in direct contact with only the DNA strand, the phosphodiester backbone of the RNA strand is inaccessible by macromolecules such as RNases. Consistent with this observation, sequence-specific recognition of an HIV-derived DNA-RNA hybrid by an engineered TALE efficiently blocked RNase H-mediated degradation of the RNA strand. Our study broadens the utility of TALE repeats and suggests potential applications in processes involving DNA replication and retroviral infections.


    Organizational Affiliation

    State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hax3
A
499Xanthomonas campestris pv. armoraciaeGene Names: hax3
Find proteins for Q3ZD72 (Xanthomonas campestris pv. armoraciae)
Go to UniProtKB:  Q3ZD72
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')G17N/A
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*UP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')H17N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 99.735α = 90.00
b = 99.735β = 90.00
c = 134.494γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references