Primary Citation PubMed: 23101623
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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.
In the inactive toggled conformation, which is visualized most clearly when the intron is crystallized in a buffer of Na + /Mg 2+ (structure 4FAX, see reference [ 30 ] and Figure 4 therein), G288 rotates by about 90° around an axis connecting its C5′ and C3′ backbone atoms, while the cytosine moiety of C377 rotates by about 70° around the glycosidic bond.
These mimic the state of the ribozyme that is released after exon ligation, and were obtained using construct OiD1-5 crystallized in the presence of different metal ions: K + /Mg 2+ (4E8M, 3.50 Å resolution), Rb + /Mg 2+ (4E8P, 3.28 Å resolution), Tl + /Mg 2+ (4E8Q, 2.84 Å resolution), Cs + /Mg 2+ (4E8R, 3.36 Å resolution), NH 4 + /Mg 2+ (4E8N, 2.96 Å resolution), Na + /Mg 2+ (4FAX, 3.10 Å resolution), and K + /Ba 2+ (4E8V, 3.99 Å resolution) [ 30 ].
Publication Year: 2013
PubMed ID is not available.
Published in 2015
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
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