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PDB ID Mentions in PubMed Central Article count: 5

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PDB ID Mentions in PubMed Central

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Now on display: a gallery of group II intron structures at different stages of catalysis.

(2013) Mob DNA 4

PubMed: 23634971 | PubMedCentral: PMC3669008 | DOI: 10.1186/1759-8753-4-14

Table 1 Available 3-D X-ray structures of the group II intron PDB id Resolution (Å) Metals Splicing stage Activity Construct Reference 4DS6 3.64 NH 4 + /Mg 2+ 5′-exon hydrolysis (pre) ... o (active site mutant) OiD1-6-G359A [ 29 ] 4FAQ 3.11 K + /Ca 2+ 5′-exon hydrolysis (pre) No (nonfunctional divalent ion) Oi5eD1-5 [ 30 ] 4FAR 2.86 K + /Mg 2+ 5′-exon hydrolysis (post) Yes Oi5eD1-5 [ 30 ] 4FAU 2.87 Li + /Mg 2+ Intermediate Partial (nonfunctional monovalent ion) Oi5eD1-5 [ 30 ] 3IGI a 3.13 K + /Mg 2+ Postcatalytic ligand-bound Yes OiD1-6 [ 26 , 27 ] 4E8M 3.50 K + /Mg 2+ Ligand-free Yes OiD1-5 [ 30 ] 4E8P 3.28 Rb + /Mg 2+ Ligand-free Yes OiD1-5 [ 30 ] 4E8R 3.36 Cs + /Mg 2+ Ligand-free Partial (nonfunctional monovalent ion) OiD1-5 [ 30 ] 4E8Q 2.84 Tl + /Mg 2+ Ligand-free Yes OiD1-5 [ 30 ] 4E8N 2.96 NH 4 + /Mg 2+ Ligand-free Yes OiD1-5 [ 30 ] 4E8V 3.99 K + /Ba 2+ Ligand-free No (nonfunctional divalent ion) OiD1-5 [ 30 ] 4FAX 3.10 Na + /Mg 2+ Ligand-free No (nonfunctional monovalent ion) OiD1-5 [ 30 ] 4FB0 3.22 K + /Mg 2+ Ligand-free Partial (active site mutant) OiD1-5-C377G [ 30 ] 4E8K b 3.03 K + /Ca 2+ SER (pre) No (nonfunctional divalent ion) OiD1-5 [ 30 ] 4E8T 3.34 K + /Ca 2+ SER (pre) No (nonfunctional divalent ion) OiD1-5 [ 30 ] 4FAW 2.70 K + /Mg 2+ SER (post) Yes OiD1-5 [ 30 ] a Additional PDB entries 3BWP, 3EOH and 3G78 represent the same form of the group II intron in the state following 3′-exon hydrolysis as 3IGI, which results from the most recent refinement.

By contrast, the structure of the post-hydrolytic state of SER was obtained using the OiD1-5 construct, bound to the same oligonucleotide used for solving 4E8K and 4E8T, but co-crystallized in the presence of physiological ions Mg 2+ and K + (structure 4FAW) [ 30 ].

They are 3EOG (3.39 Å resolution) [ 31 ], 4E8K (3.03 Å resolution) [ 30 ], 4E8T (3.34 Å resolution) [ 30 ], and 4FAW (2.70 Å resolution), respectively [ 30 ].

Publication Year: 2013


Solving nucleic acid structures by molecular replacement: examples from group II intron studies.

(2013) Acta Crystallogr D Biol Crystallogr 69

PubMed: 24189228 | PubMedCentral: PMC3817690 | DOI: 10.1107/S0907444913013218

We implemented this strategy using Phaser (McCoy, 2007 ▶ ) and a more recent data set (PDB entry 4faw ; Marcia & Pyle, 2012 ▶ ).

Phasing attempts in Phaser (McCoy, 2007 ▶ ) using the experimental structure-factor amplitudes of the structure with PDB code 4faw (Marcia & Pyle, 2012 ▶ ) were successful with both sets of models, having r.m.s.d. values of up to 2–3 Å from the original (Fig. 2 ▶ ).

( a ) The experimental structure-factor amplitudes of an O. iheyensis group II intron data set (PDB entry 4faw ) can be phased with a Phaser multi-domain MR search using ten individual intron subdomains as a starting model.

We then performed MR runs in Phaser , attempting to phase the experimental structure-factor amplitudes of PDB entry 4faw .

Publication Year: 2013


RNA Bricks--a database of RNA 3D motifs and their interactions.

(2014) Nucleic Acids Res 42

PubMed: 24220091 | PubMedCentral: PMC3965019 | DOI: 10.1093/nar/gkt1084

Among 20 motifs, 16 were derived from RNA structures annotated as tRNA, 3 as tRNASec and 1 as group-II-D1D4-3 (PDB: 4FAW).

We also found a T-loop like motif in a representative of a group-II-D1D4-3 family (PDB: 4FAW).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4356372

As a result, many recurrent motifs in the resulting model were originally extracted from other models of group II introns ( e.g. PDB entry 4faw ), which clearly biased the results.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4455060

To structurally compare the loops, hydrogen atoms were added to Protein Data Bank (PDB) X-ray structures of the group II intron (3EOH, 4E8M, 4E8Q, 4FAR, 4FAW, and 4FAX) using Reduce with the NOFLIP op... ion.

Publication Year: 2015