4GG4 | pdb_00004gg4

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

• PDB DOI: https://doi.org/10.2210/pdb4GG4/pdb
• NAKB: 4GG4

• Classification: DNA BINDING PROTEIN/DNA/RNA
• Organism(s): Xanthomonas campestris pv. armoraciae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-08-05 Released: 2012-10-03 
• Deposition Author(s): Yin, P., Deng, D., Yan, C.Y., Pan, X.J., Yan, N., Shi, Y.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.243 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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

• PubMed: 23022487 
• DOI: https://doi.org/10.1016/j.celrep.2012.09.001
• Primary Citation Related Structures: 
  4GG4


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.45 kDa 
• Atom Count: 4,265 
• Modeled Residue Count: 521 
• Deposited Residue Count: 533 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hax3	A	499	Xanthomonas campestris pv. armoraciae	Mutation(s): 18  Gene Names: hax3
UniProt
Find proteins for Q3ZD72 (Xanthomonas campestris pv. armoraciae) Explore Q3ZD72  Go to UniProtKB:  Q3ZD72

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')	B [auth G]	17	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*UP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')	C [auth H]	17	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.243 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.735	α = 90
b = 99.735	β = 90
c = 134.494	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Yin, P., Deng, D., Yan, C.Y., Pan, X.J., Yan, N., Shi, Y.G.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description