Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 5

Citations in PubMed

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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.

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Promoting RNA helical stacking via A-minor junctions.

(2011) Nucleic Acids Res 39

PubMed: 20876687 | PubMedCentral: PMC3035441 | DOI: 10.1093/nar/gkq748

( F ) Bulged-G/helix A-minor junction (A-minor 3WJ_ACD junction): Oceanobacillus iheyensis Group II intron (PDB ID: 3BWP).

Publication Year: 2011


Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.

(2012) J Biomol NMR 53

PubMed: 22714631 | PubMedCentral: PMC3405240 | DOI: 10.1007/s10858-012-9642-5

Despite sequence differences, the bulge conformation in the full intron will probably be similar to the more recent X-ray structures of the full Oceanobacillus iheyensis self-spliced group IIC intron ... here tertiary interactions stabilize a different bulge conformation (PDBs: 3BWP, 3EOG, 3EOH, and 3IGI) (Toor et al.

Publication Year: 2012


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.

Publication Year: 2013


RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.

(2014) Nucleic Acids Res 42

PubMed: 24771339 | PubMedCentral: PMC4086112 | DOI: 10.1093/nar/gku330

They concern the structure of unknotted RNA signal recognition particle (3NDB), and knotted RNAs of 30S ribosome unit from Escherichia Coli (1PNX), bacterial RNase P (3DHS) and two group IIC introns (... FAU and 3BWP).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4356372

One model was the group II intron structure (PDB entry 3bwp ) solved at 3.1 Å resolution (Toor et al. , 2008 ▶ ).

Publication Year: 2015