Citations in PubMed

Primary Citation PubMed: 22223736 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 11

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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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.

Publication Year: 2013


Quantitative analysis of TALE-DNA interactions suggests polarity effects.

(2013) Nucleic Acids Res 41

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 ).

Publication Year: 2013


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.

Publication Year: 2013


TAL effectors specificity stems from negative discrimination.

(2013) PLoS One 8

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) [19] and DNA-bound (PDB codes: 3UGM, 3V6T) [18] , [19] TAL effectors were used to bu... ld model systems in the framework of classical molecular mechanics [24] .

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 [18] (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 [19] (PDB codes: 3V6T, 3V6P).

Publication Year: 2013


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.

(2013) PLoS One 8

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.

Publication Year: 2013


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).

Publication Year: 2013


TALE-PvuII fusion proteins--novel tools for gene targeting.

(2013) PLoS One 8

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.

Publication Year: 2013


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 [41] .

Publication Year: 2014


TALEs from a spring--superelasticity of Tal effector protein structures.

(2014) PLoS One 9

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).

Publication Year: 2014