3UGM

Structure of TAL effector PthXo1 bound to its DNA target

• PDB DOI: https://doi.org/10.2210/pdb3UGM/pdb
• NAKB: 3UGM

• Classification: TRANSCRIPTION/DNA
• Organism(s): Xanthomonas oryzae pv. oryzae PXO99A
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-11-02 Released: 2012-01-04 
• Deposition Author(s): Mak, A.N.S., Bradley, P., Cernadas, R.A., Bogdanove, A.J., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.294 
• R-Value Work: 0.266 

Literature

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target.

Mak, A.N., Bradley, P., Cernadas, R.A., Bogdanove, A.J., Stoddard, B.L.

(2012) Science 335: 716-719

• PubMed: 22223736 
• DOI: https://doi.org/10.1126/science.1216211
• Primary Citation of Related Structures:  
  3UGM


• PubMed Abstract: 
  

  DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs). The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization. Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA. The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove. The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand. Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition.

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Organizational Affiliation: 

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025 Seattle, WA 98019, USA.

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: 132.29 kDa 
• Atom Count: 7,853 
• Modelled Residue Count: 930 
• Deposited Residue Count: 1,123 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TAL effector AvrBs3/PthA	A	1,047	Xanthomonas oryzae pv. oryzae PXO99A	Mutation(s): 8  Gene Names: pthXo1, PXO_00227
UniProt
Find proteins for B2SU53 (Xanthomonas oryzae pv. oryzae (strain PXO99A)) Explore B2SU53  Go to UniProtKB:  B2SU53

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA-1	B	38	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA-2	C	38	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.294 
• R-Value Work: 0.266 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.578	α = 90
b = 248.481	β = 90
c = 54.646	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASES	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-04 
Deposition Author(s): Mak, A.N.S., Bradley, P., Cernadas, R.A., Bogdanove, A.J., Stoddard, B.L.

Revision History  

• Version 1.0: 2012-01-04
  Type: Initial release
  
• Version 1.1: 2012-01-25
  Changes: Database references
• Version 1.2: 2012-02-22
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references