Primary Citation PubMed: 22682761
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Synthesis and gene silencing properties of siRNAs containing terminal amide linkages.
(2014) Biomed Res Int 2014
PubMed: 24791003 | PubMedCentral: PMC3984766 | DOI: 10.1155/2014/901617
Molecular Docking The miR-20a/hAgo 2 three-dimensional structure was downloaded from the Protein Data Bank (PDB code 4F3T) [ 9 ].
In particular, the chimeric 3′-OH-PNA AS of siRNA 17 (oligomer O) and the AS of "5′-capped" siRNA 16 (oligomer M)” were docked in the recently published structure of hAgo 2 in complex with miR-20a (PDB code 4F3T) [ 9 ].
Publication Year: 2014
Bioenergetics and gene silencing approaches for unraveling nucleotide recognition by the human EIF2C2/Ago2 PAZ domain.
(2014) PLoS One 9
PubMed: 24788663 | PubMedCentral: PMC4008379 | DOI: 10.1371/journal.pone.0094538
The coordinates of interaction were derived from PDB ID 4EI1 and 4F3T.
The crystal structure of human EIF2C2/Ago2 was resolved when either uridine or guanosine nucleotides were bound to the PAZ domain (PDB ID 4EI1 and 4F3T, respectively).
The coordinates of interaction were derived from PDB ID 4F3T.
Cooperative gene regulation by microRNA pairs and their identification using a computational workflow.
(2014) Nucleic Acids Res 42
PubMed: 24875477 | PubMedCentral: PMC4081082 | DOI: 10.1093/nar/gku465
Therefore, we utilized the structure of human argonaute-2 (hAgo2) in complex with miR-20a previously generated by Elkayam et al. ( 24 ) at 2.2 Å resolution (PDB ID: 4F3T) as basis for ... D modeling.
3D structure modeling and MDS 3D model design For the detailed 3D model of two miRNA-Argonaute hybrids (miR-20a/hAgo2) attached to one stretch of target 3′ UTR (NEURL1B mRNA) we retrieved the crystal structure of miR-20a/hAgo2 determined by Elkayam et al. ( 24 ) through X-ray crystallography from the Protein Data Bank (PDB id: 4F3T).
DBBP: database of binding pairs in protein-nucleic acid interactions.
(2014) BMC Bioinformatics 15 Suppl 15
PubMed: 25474259 | PubMedCentral: PMC4271565 | DOI: 10.1186/1471-2105-15-S15-S5
As an example, Figure 1 shows three H-bonds between Threonine (Thr224) and Cytosine (C8) in a protein-RNA complex (PDB ID: 4F3T) [ 19 ].
Figure 2 shows the structure of the protein-RNA complex (PDB ID: 4F3T).
Three H-bonds between Cytosine (C8) and Threonine (Thr224) of a protein-RNA complex (PDB ID: 4F3T).
Figure 2 The structure of a protein-RNA complex (PDB ID: 4F3T) .
Molecular evolution and diversification of the Argonaute family of proteins in plants.
(2015) BMC Plant Biol 15
PubMed: 25626325 | PubMedCentral: PMC4318128 | DOI: 10.1186/s12870-014-0364-6
Additionally, 5 AGO sequences from Tribolium castaneum, 32 AGO sequences (including AGO1 and AGO2) from insects and early branching animals (e.g. sponges, cnideria), and one each of HsAGO2 (PDB code: ... F3T) and KpAGO (PDB code: 4F1N) (for a total of 302 sequences from 66 species; Additional files 1 ; detailed in methods section) were used as the out-group in this analysis.
Among all the plant AGOs known, the structure of only the MID domain of AtAGO1, 2 and 5 has been resolved to date [ 22 ] Human AGO2 (PDB code 4F3T, chain A) was the best template for most of the NaAGOs.
ClusPro server ( http://cluspro.bu.edu/login.php ) [ 60 ] was used to dock the 20nt RNA (PDB code 4F3T, chain R) to all four NaAGOs.
Fig A, B, C and D show the interaction and position of the first oxygen atom of 5' P-U residue of RNA (PDB code 4F3T, chain R) in the lobe formed by MID-PIWI domain of NaAGO1a, NaAGO5, NaAGO2 and NaAGO4a, respectively.
Additionally, 5 AGOs from T. castaneum, and 1 each from Human (PDB code 4F3T) and K. polysporus (PDB code 4F1N) were also used (as out groups) to create the ‘AGO dataset I’, comprising a total of 270 AGO sequences.
Publication Year: 2015
PubMed ID is not available.
Published in 2015
The input miRNA structure was modeled using ModeRNA[ 83 ] based on miRNA fragments in the crystal structure (PDB ID: 4F3T).
S12 Fig The partially open conformation of hAgo2 in the co-crystal structure (PDB ID:4F3T) cannot accommodate miRNA.
The restraints were selected from the closest contacts between hAgo2 and terminal nucleotides of miRNA in the crystal structure (PDB ID: 4F3T).
MD simulations of WT hAgo2 (blue) and the mutants were initiated from three conformations: (A) a closed conformation, (B) a partially open conformation extracted from the binary hAgo2-miRNA crystal structure (PDB ID: 4F3T) and (C) an open conformation.
Methods MD simulation setup The initial apo hAgo2 conformation was taken from the crystal structure of hAgo2 in complex with miR-20a (PDB ID: 4F3T)[ 32 ], and the missing residues were added using MODELLER[ 70 – 73 ].
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