Primary Citation PubMed: 22223736
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Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains.
(2012) Nat Commun 3
PubMed: 22828628 | PubMedCentral: PMC3556390 | DOI: 10.1038/ncomms1962
We based our calculations on the recently released crystal structure of the TALE PthXo1 bound to DNA (PDB ID: 3UGM) 12 .
Publication Year: 2012
Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants.
(2013) PLoS One 8
PubMed: 23472078 | PubMedCentral: PMC3589468 | DOI: 10.1371/journal.pone.0057286
(C) Structure of 2 TALE repeats (residues 624–691; PDB: 3UGM).
Publication Year: 2013
Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats.
(2013) Nucleic Acids Res 41
PubMed: 23408850 | PubMedCentral: PMC3627573 | DOI: 10.1093/nar/gkt080
The colour code can be deduced from the scheme, I-SceI in green, the TALE protein in red (only the 23 repeats of the 3UGM structure are shown) and MutH in blue.
Quantitative analysis of TALE-DNA interactions suggests polarity effects.
PubMed: 23408851 | PubMedCentral: PMC3627578 | DOI: 10.1093/nar/gkt085
The PthXol-DNA (3UGM) crystal structure depicts one additional repeat-like module, the ‘-1 repeat’, contacting the conserved 5′-T, but no well-ordered structures or DNA contact... are observed N-terminal to that ( 5 ).
Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism.
(2013) Acta Crystallogr D Biol Crystallogr 69
PubMed: 23999294 | PubMedCentral: PMC3760130 | DOI: 10.1107/S0907444913016429
( d ) Superposition of the PthXo1 (purple; PDB entry 3ugm ; Mak et al. , 2012 ▶ ), dHax3 (yellow; PDB entry 3v6t ; Deng et al. , 2012 ▶ ) and AvrBs3 (orange) protein structures.
TAL effectors specificity stems from negative discrimination.
PubMed: 24282528 | PubMedCentral: PMC3840011 | DOI: 10.1371/journal.pone.0080261
Materials and Methods Molecular dynamics simulations The available crystal structures of both free (PDB code: 3V6P)  and DNA-bound (PDB codes: 3UGM, 3V6T)  ,  TAL effectors were used to bu... ld model systems in the framework of classical molecular mechanics  .
Mak et al. obtained the structure of PthXo1, a naturally-occurring 23.5 repeats TAL bound to its corresponding DNA target, at 3 Å resolution  (PDB code: 3UGM), while Deng et al. solved the structure of a designed 11.5 repeats TAL system in both bound and unbound states with resolutions of 1.85 Å and 2.5 Å respectively  (PDB codes: 3V6T, 3V6P).
TAL effector specificity for base 0 of the DNA target is altered in a complex, effector- and assay-dependent manner by substitutions for the tryptophan in cryptic repeat -1.
PubMed: 24312634 | PubMedCentral: PMC3849474 | DOI: 10.1371/journal.pone.0082120
The structure of PthXo1 bound to its natural target site (PDB ID: 3UGM) was used as a modeling template.
g001 Figure 1 Alignment of N-terminal portions of multiple TAL effector crystal structures shows a conserved conformation for W232 consistent with an important interaction with the 0 th position T. The N terminus of TAL effector PthXo1 bound to its DNA target (PDB structure 3UGM) [ 4 ] is shown in blue, the N terminus of unbound artificial TAL effector dTALE2 (PDB structure 4HPZ) [ 26 ] in red, and the N terminus of artificial TAL effector dHAX3 bound to a DNA-RNA hybrid (PDB structure 4GG4) [ 5 ] in brown.
Newer gene editing technologies toward HIV gene therapy.
(2013) Viruses 5
PubMed: 24284874 | PubMedCentral: PMC3856413 | DOI: 10.3390/v5112748
( A ) Crystal structure of a TALEN complexed with the target DNA fragment (PDB ID: 3UGM, modeled by UCSF chimera software).
TALE-PvuII fusion proteins--novel tools for gene targeting.
PubMed: 24349308 | PubMedCentral: PMC3857828 | DOI: 10.1371/journal.pone.0082539
This model was constructed by aligning the structures of the individual proteins [pdb 1pvi [ 74 ] and pdb 3ugm [ 76 ]] on a DNA composed of the PvuII recognition site and two TALE target sites up- and... downstream of the PvuII recognition site, separated by 6 bp.
Cell-penetrating peptide-mediated delivery of TALEN proteins via bioconjugation for genome engineering.
(2014) PLoS One 9
PubMed: 24465685 | PubMedCentral: PMC3896395 | DOI: 10.1371/journal.pone.0085755
PDB ID: 3UGM  .
Publication Year: 2014
TALEs from a spring--superelasticity of Tal effector protein structures.
PubMed: 25313859 | PubMedCentral: PMC4196931 | DOI: 10.1371/journal.pone.0109919
Methods We considered the structures of two TALE proteins, that of the artificially engineered dHax3 in its DNA-free form (PDB ID 3V6P) and in a conformation determined in the presence of DNA (3V6T), ... nd that of PthXo1 from the rice pathogen Xanthomonas oryzae which was co-crystallized with its DNA target (3UGM).
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