Primary Citation PubMed: 23101623
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
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.
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
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.