PDBsum entry 1k5i

RNA

PDB id

1k5i

Loading ...

Contents

			DNA/RNA

PDB id:

1k5i

Links

Name:

RNA

Title:

Nmr structure of a ribosomal RNA hairpin containing a conserved cucaa pentaloop

Structure:

5'-r(p Gp Gp Ap Cp Cp Cp Gp Gp Gp Cp Up Cp Ap Ap Cp Cp Up G p Gp Gp Up Cp C)-3'. Chain: a. Fragment: 16s ribosomal RNA fragment (612-628). Engineered: yes. Other_details: cucaa pentaloop

Source:

Synthetic: yes. Other_details: the oligonucleotide was synthesized by t7 run-off transcription.

NMR struc:

10 models

Authors:

U.Nagaswamy,X.Gao,S.A.Martinis,G.E.Fox

Key ref:

U.Nagaswamy et al. (2001). NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop. Nucleic Acids Res, 29, 5129-5139. PubMed id: 11812846 DOI: 10.1093/nar/29.24.5129

Date:

10-Oct-01

Release date:

17-Oct-01

	Headers

	References

DNA/RNA chain

G-G-A-C-C-C-G-G-G-C-U-C-A-A-C-C-U-G-G-G-U-C-C 23 bases

DOI no: 10.1093/nar/29.24.5129	Nucleic Acids Res 29:5129-5139 (2001)
PubMed id: 11812846

NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop.
U.Nagaswamy, X.Gao, S.A.Martinis, G.E.Fox.

ABSTRACT

The structure of a 23 nt RNA sequence, rGGACCCGGGCUCAACCUGGGUCC, was elucidated using homonuclear NMR, distance geometry and restrained molecular dynamics. This RNA is analogous to residues 612-628 of the Escherichia coli 16S rRNA. The structure of the RNA reveals the presence of a pentaloop closed by a duplex stem in typical A-form conformation. The loop does not form a U-turn motif, as previously predicted. A non-planar A.C.A triple base interaction (hydrogen bonds A13 NH6-C10 O2 and C10 N3-A14 NH6) stabilizing the loop structure is inferred from structure calculations. The CUCAA loop structure is asymmetrical, characterized by a reversal of the phosphodiester backbone at the UC step (hydrogen bond C12 NH4-C10 O2') and 3'-stacking within the CAA segment. Loop base U11 is oriented towards the major groove and the consecutive adenosines on the 3'-end of the loop are well stacked, exposing their reactive functional groups in the minor groove defined by the duplex stem. The solution structure of the loop resembles that seen in the 3.3 A X-ray structure of the entire 30S subunit, where the analogous loop interacts with a ribosomal protein and a receptor RNA helix.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21469161

E.J.Denning, U.D.Priyakumar, L.Nilsson, and A.D.Mackerell (2011).
Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

J Comput Chem, 32, 1929-1943.

16425174

L.Grajcar, C.El Amri, M.Ghomi, S.Fermandjian, V.Huteau, R.Mandel, S.Lecomte, and M.H.Baron (2006).
Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy.

Biopolymers, 82, 6.

15939932

Q.Zhao, U.Nagaswamy, H.Lee, Y.Xia, H.C.Huang, X.Gao, and G.E.Fox (2005).
NMR structure and Mg2+ binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S ribosomal subunit.

Nucleic Acids Res, 33, 3145-3153.

PDB code:

2hem

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.