Citations in PubMed

Primary Citation PubMed: 357742 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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Crystal structure of human selenocysteine tRNA.

(2009) Nucleic Acids Res 37

PubMed: 19692584 | PubMedCentral: PMC2764427 | DOI: 10.1093/nar/gkp648

Partial structures from the tRNA Asp and tRNA Phe coordinates [PDB ID: 2TRA ( 34 ) and 6TNA ( 35 )] were used as the search models.

Publication Year: 2009


Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.

(2009) Bioinformatics 25

PubMed: 19812110 | PubMedCentral: PMC2788923 | DOI: 10.1093/bioinformatics/btp576

We show both a full atomic stick and a cartoon representation for each of the following tRNA structures: the full atomic crystal structure (PDB ID 6TNA) ( A ), a full atomic model generated by C2A usi... g the ideal backbone from the crystal structure ( B ), a full atomic model based on the NAST tRNA model A ( C ), model B ( D ), and model C ( E ).

Yeast phenylalanine tRNA (‘tRNA’, PDB ID 6TNA) 76 residues (Sussman et al .

RMSD of minimized full atomic structures Molecule Overall Helical Non-helical ID RMSD (Å) fragments fragments RMSD (Å) RMSD (Å) Validation structures (10 models) 1KXK 2.13 ± 0.21 1.36 ± 0.44 2.41 ± 1.39 6TNA 2.81 ± 0.11 1.10 ± 0.09 3.02 ± 1.27 3CUL 3.06 ± 0.18 1.77 ± 0.82 2.48 ± 1.90 1GID 3.16 ± 0.08 2.03 ± 1.22 2.75 ± 1.45 1ZZN 2.79 ± 0.16 2.10 ± 0.74 2.56 ± 1.42 1Y0Q 2.76 ± 0.07 1.92 ± 0.68 2.50 ± 1.54 NAST tRNA models (50 models) Model A 8.39 ± 0.27 2.65 ± 0.71 4.13 ± 1.91 Model B 13.30 ± 0.31 3.08 ± 1.28 3.82 ± 1.51 Model C 15.99 ± 0.76 3.06 ± 1.13 4.19 ± 1.95 We report both overall RMSD values and separate values for helical and non-helical fragments.

Evaluation of minimized full atomic structures with MolProbity and the RCSB ADIT tool Molecule ID MolProbity RCSB ADIT Clashscore (goal=0) Percentile ( N =1784) Covalent bonds Covalent angles Crystal structure Best model Average (10 models) Crystal structure Best model Average (10 models) RMSD (Å) RMSD (degrees) Crystal Models Crystal Models 1KXK 14.03 3.33 8.54 ± 5.54 54 97 78.30 ± 22.53 0.006 0.017 0.9 2.8 6TNA 26.46 4.92 9.11 ± 4.54 19 94 76.60 ± 19.10 0.079 0.017 3.4 2.7 3CUL 7.67 6.11 8.56 ± 2.30 83 90 79.10 ± 10.81 0.007 0.020 1.0 3.2 1GID 35.78 13.31 23.21 ± 14.67 10 57 35.80 ± 18.36 0.009 0.031 0.9 3.4 1ZZN 32.67 15.29 29.46 ± 9.82 13 48 21.11 ± 16.00 0.008 0.032 1.1 3.6 1Y0Q 40.47 15.9 40.82 ± 17.72 8 46 13.60 ± 15.03 0.007 0.036 1.0 3.8 We give MolProbity Clashscores and percentiles for validation structures.

Publication Year: 2009


A coarse-grained force field for Protein-RNA docking.

(2011) Nucleic Acids Res 39

PubMed: 21846771 | PubMedCentral: PMC3241652 | DOI: 10.1093/nar/gkr636

Results for docking with unbound structures Complex Receptor Ligand br:bl ur:bl br:ul ur:ul 1DFU mn : p 364D abc (2.8) 1B75 (3.8) 3 1 −[18] −[4] 1JBR d : b 430D a (2.8) 1AQZ a (0.6) 14... 18 30[2] 100 1K8W b : a 2K4C (2.8) 1R3F a (1.5) 1 – 2[1] – 1TTT d : a 6TNA a (2.6) 1TUI a (10.1) 1 −[480] 291 – 2RKJ c : a , b 1Y0Q a (2.6) 1Y42 aa (1.1) 2 −[13] −[>1k] −[>1k] 2AZ2 cd : ab model (1.4) 2B9Z (1.5) 3 3[1] >1k[349] >1k[43] 2E9T bc : a model (3.3) 1U09 a (0.8) 2 −[712] >1k −[-] Subscripts at PDB id denote involved chains, numbers in brackets correspond to RMSD (P atoms for receptor and Cα for ligand) versus bound structure (in case of multiple NMR models an average value is provided); br, bl, ur, ul—bound/unbound receptor/ligand; numbers correspond to the ranks of ‘hits’ or ‘acceptable’ solutions (in square brackets).

Publication Year: 2011


NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules.

(2012) Nucleic Acids Res 40

PubMed: 22661578 | PubMedCentral: PMC3394293 | DOI: 10.1093/nar/gks513

The standard NASSAM search for base triples and MC-annotate annotations for the structures of a tRNA (PDB ID: 6TNA) and a bacterial ribonuclease P holoenzyme in complex with tRNA (PDB ID: 3Q1R) were a... le to accurately identify the A23.U12.A9 ( Figure 1 ) base triples in 6TNA as well as the A23.U12.A9 in the tRNA component and a G161.C177.G172 triple in 3Q1R ( Table 1 ).

Publication Year: 2012


Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase.

(2012) Nucleic Acids Res 40

PubMed: 22923517 | PubMedCentral: PMC3488237 | DOI: 10.1093/nar/gks790

( B ) Ribbon diagram of yeast free tRNA Phe (PDB accession code 6TNA) ( 40 ), with the same color-coding as in (A).

Publication Year: 2012


tRNA binding to antitumor drug doxorubicin and its analogue.

(2013) PLoS One 8

PubMed: 23922696 | PubMedCentral: PMC3726733 | DOI: 10.1371/journal.pone.0069248

g007 Figure 7 Best conformations for drug docked to tRNA (PDB entry 6TNA).

t001 Table 1 Ribonucleotides in the vicinity of DOX and FDOX docked with tRNA (PDB 6TNA) and the free binding energies of the docked complexes.

tRNA structure were obtained from the PDB (ID: 6TNA) [29] and the three dimensional structures of DOX and FDOX were generated from PM3 semi-empirical calculations using Chem3D Ultra 6.0.

Publication Year: 2013


MD simulation studies to investigate iso-energetic conformational behaviour of modified nucleosides m(2)G and m(2) 2G present in tRNA.

(2013) Comput Struct Biotechnol J 5

PubMed: 24688708 | PubMedCentral: PMC3962230 | DOI: 10.5936/csbj.201302015

pdb 6TNA.

Torsion angle β ( Fig. 4B ) maintains starting geometry ±180° [ 18 ] with small fluctuations at ± 60° as found in crystal structure 6TNA.

pdb [ 33 ] and 6TNA.

Publication Year: 2013


Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors.

(2014) Front Genet 5

PubMed: 24822055 | PubMedCentral: PMC4013460 | DOI: 10.3389/fgene.2014.00109

(B) L-shape tertiary structure of cloverleaf tRNA ( Saccharomyces cerevisiae tRNA Phe , PDB code 6TNA).

Publication Year: 2014


COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures.

(2014) Nucleic Acids Res 42

PubMed: 24831543 | PubMedCentral: PMC4086061 | DOI: 10.1093/nar/gku438

An example of a base triple is provided in Figure 1A where a base triple with four hydrogen bonds is part of a transfer RNA structure (PDB ID: 6tna).

ACCESSION NUMBERS PDB IDs: 6tna, 4erl and 4erj.

( A ) Base triple interaction example A9.A23.U12 from the yeast tRNA Phe structure (PDB ID: 6tna, left panel) and it's corresponding representation in a connection table (right panel).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4191394

Simulation details Initial coordinates were derived from the crystal structure (PDB 6TNA), changing modified residues to their unmodified analogs.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4191411

( B ) Best conformations for polyamines docked to tRNA (PDB entry 6TNA).

Publication Year: 2014