Primary Citation PubMed: 10913310
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The electrostatic characteristics of G.U wobble base pairs.
(2007) Nucleic Acids Res 35
PubMed: 17526525 | PubMedCentral: PMC1920249 | DOI: 10.1093/nar/gkm274
However, for some G·U pairs (for example, 1HLX and 1EKA), the formal major groove electrostatic potential is less negative than their canonical counterparts.
RNA structures from the PDB utilized in the Poisson–Boltzmann calculations PDB code Sequences Structural features 1AJF 5′GACAGGGGA Tandem G·U; Motif III; P5b helix of Group I intron ( 51 ) 3′CUGUUUCAA 1C0O 5′GGGUCUU Tandem G·U; Motif II; P5 helix of Group I intron ( 50 ) 3′CCUGGGC 1DFU 5′CCCAUGCGAGAGUAGGGAC Tandem G·U; Motif I; 5SrRNA/L25 complex ( 49 ) 3′GGGGUGUGAUGGUAGCCGU 1EKA 5′GAGUGCUC Tandem G·U; Motif I; NMR structure ( 32 ) 3′CUCGUGAG 1GUC 5′GAGGUCUC Tandem G·U; Motif II; NMR structure ( 34 ) 3′CUCUGGAG 1HLX 5′GGGAUAACUU Single G·U; P1 helix of Group I intron ( 23 ) 3′CCCUGUUGGC 1IKD a 5′GGGGCUCUU Single G·U; acceptor stem of E. coli tRNA Ala ( 24 ) 3′CCUCGAGGC 1QES 5′GGAGUUCC Tandem G·U; Motif II; NMR structure ( 17 ) 3′CCUUGAGG 1QET 5′GGAUGUCC Tandem G·U; Motif I; NMR structure ( 17 ) 3′CCUGUAGG 315D 5′GUAUGUAC Tandem G·U, Motif I; Crystal Structure ( 78 ) 3′CAUGUAUG 433D b 5′GGUAUUGCGGUACC Two tandem G·U, Motif III; Crystal structure ( 52 ) 3′CCAUGGCGUUAUGG 434D 5′UAGCUCC 3′AUCGGGG Single G·U; Crystal structure of acceptor stem of E. coli tRNA Ala ( 26 ) 472D 5′GUGUUUAC Tandem G·U, Motif III; Crystal structure ( 33 ) 3′CACGGAUG 435D 5′UAGCCCC 3′AUCGGGG Mutant of 434D, where G3·U70 was replaced by G3-C70 ( 26 ) a The unpaired bases in 1IKD were truncated for easy comparison with its WC RNA counterparts.
Total electrostatic potentials (EP in kT/e) of the G·U pairs embedded in RNA helices, compared with their canonical counterparts RNA helices EP at the major groove EP at the minor groove GU GC AU GU GC AU Single G·U 1HLX −4.0 −4.1 −4.0 −1.3 −0.3 −0.5 1IKD −5.9 −3.9 −4.2 0.0 −0.1 −0.4 434D a −5.1 −4.0 −4.1 0.7 0.0 −0.3 Motif I 1EKA −3.5 −4.4 −3.6 −1.4 −0.1 −0.3 1QET −4.7 −4.4 −3.8 −0.6 −0.2 −0.5 315D −4.5 −4.4 −3.8 −0.7 −0.2 −0.5 Motif II 1C0O −5.9 −3.7 −3.9 −1.0 0.2 −0.1 1GUC −6.3 −3.9 −4.0 0.1 −0.3 −0.2 1QES −5.1 −4.1 −4.1 0.7 0.0 −0.3 Motif III 1AJF −5.3 −4.4 −4.4 −0.7 −0.2 −0.6 433D −4.9 −4.5 −4.4 −0.9 −0.2 −0.6 472D −5.9 −4.0 −3.8 −1.0 −0.1 −0.3 a Note that the structure of the canonical form of 434D, where the G3·U70 was replaced by G3C70, was already determined by X-ray crystallography (PDB code: 435D).
The surface electrostatic potential maps of RNA helices with ( A ) Motif I G·U pairs (PDB:1EKA), ( B ) Motif II G·U pairs (PDB:1GUC) and ( C ) Motif III G·U pairs (PDB:472D).
Publication Year: 2007
PubMed ID is not available.
Published in 2015
RNA dataset: details and length of MD simulations System PDB code Chain length Simulation time (µs) Duplex 1EKA 16 1.0 Sarcin-ricin domain 1Q9A 25 0.9 Hammerhead ribozyme 301D 41 0.25 add ribo... witch 1Y26 71 0.25 thiM r iboswitch 2GDI 78 N.A. For the thiM riboswitch, no MD was performed.
Publication Year: 2015
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