DSSR-enabled G4 identification/annotation: PDB entry 1my9
Summary information and primary citation
- PDB-id
- 1my9
- Class
- RNA
- Method
- NMR
- Summary
- Solution structure of a k+ cation stabilized dimeric RNA quadruplex containing two g:g(:a):g:g(:a) hexads, g:g:g:g tetrads and uuuu loops
- Reference
- Liu H, Matsugami A, Katahira M, Uesugi S (2002): "A Dimeric RNA Quadruplex Architecture Comprised of Two G:G(:A):G:G(:A) Hexads, G:G:G:G Tetrads and UUUU Loops." J.Mol.Biol., 322, 955-970. doi: 10.1016/S0022-2836(02)00876-8.
- Abstract
- Using CD and NMR, we determined the structure of an RNA oligomer, r(GGAGGUUUUGGAGG) (R14), comprising two GGAGG segments joined by a UUUU segment. A modified quadruplex structure was observed for r(GGAGGUUUUGGAGG) in solution even in the absence of K(+). An unusually stable dimeric RNA quadruplex architecture formed from two strands of r(GGAGGUUUUGGAGG) at low K(+) concentration is reported here. In each strand of r(GGAGGUUUUGGAGG), two sets of successive turns in the GGAGG segments and turns at both ends of the UUUU loops drive four G-G steps to align in a parallel manner, a core with two stacked G-tetrads being formed. Two adenine bases bind to two edges of one G:G:G:G tetrad through the sheared G:A mismatch augmenting the tetrad into a G:G(:A):G:G(:A) hexad. Thus, one molecule of r(GGAGGUUUUGGAGG) folds into a modified quadruplex comprising a G:G:G:G tetrad, a UUUU double-chain reversal loop and a G:G(:A):G:G(:A) hexad. Two such molecules further associate by stacking through the dimeric hexad-hexad interface with a rotational symmetry. The ribose rings of most nucleotides take S (close to C2'-endo) puckering, which is unusual for an RNA. K(+) can increase the stability of this quadruplex structure; the number of bound K(+) was estimated from the results of the titration experiment. Besides G:G and G:A mismatches, a network of hydrogen bonds including O4'-NH(2) and C-H..O hydrogen bonds, and the extensive base stacking contribute to the high thermodynamic stability of R14. Our results could provide the stereochemical and thermodynamic basis for elucidating the biological role of the GGAGG-containing RNA segments abundantly existing in various RNAs. Relevance to quadruplex-mediated mRNA-FMRP binding and HIV-1 genome RNA dimerization is discussed.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, 2(-P-P-P), coaxial interfaces: 5'/5'
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.448 type=other O+ nts=4 GGGG A.G1,A.G4,A.G10,A.G13 2 glyco-bond=---- sugar=-.-- groove=---- planarity=0.841 type=other O+ nts=4 GGGG A.G2,A.G5,A.G11,A.G14 3 glyco-bond=---- sugar=---- groove=---- planarity=0.435 type=other O+ nts=4 GGGG B.G15,B.G18,B.G24,B.G27 4 glyco-bond=---- sugar=-3-- groove=---- planarity=0.717 type=saddle O+ nts=4 GGGG B.G16,B.G19,B.G25,B.G28
List of 1 G4-helix
In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.
Helix#1, 4 G-tetrads, inter-molecular, with 2 stems
|
1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major O+ nts=4 GGGG A.G2,A.G5,A.G11,A.G14 2* glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.G1,A.G4,A.G10,A.G13 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.G18,B.G15,B.G27,B.G24 4 glyco-bond=---- sugar=3--- groove=---- Major-->WC O+ nts=4 GGGG B.G19,B.G16,B.G28,B.G25 step#1 mp(<<,backward) area=10.94 rise=3.87 twist=29.0 step#2 mm(<>,outward) area=13.44 rise=3.66 twist=9.2 step#3 pm(>>,forward) area=9.00 rise=4.04 twist=32.8 strand#1 RNA glyco-bond=---- sugar=---3 nts=4 GGGG A.G2,A.G1,B.G18,B.G19 strand#2 RNA glyco-bond=---- sugar=.--- nts=4 GGGG A.G5,A.G4,B.G15,B.G16 strand#3 RNA glyco-bond=---- sugar=---- nts=4 GGGG A.G11,A.G10,B.G27,B.G28 strand#4 RNA glyco-bond=---- sugar=---- nts=4 GGGG A.G14,A.G13,B.G24,B.G25 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major O+ nts=4 GGGG A.G2,A.G5,A.G11,A.G14 |
|
2* glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.G1,A.G4,A.G10,A.G13 |
|
3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.G18,B.G15,B.G27,B.G24 |
List of 2 G4-stems
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.
Stem#1, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.G1,A.G4,A.G10,A.G13 2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major O+ nts=4 GGGG A.G2,A.G5,A.G11,A.G14 step#1 pm(>>,forward) area=10.94 rise=3.87 twist=29.0 strand#1 U RNA glyco-bond=-- sugar=-- nts=2 GG A.G1,A.G2 strand#2 U RNA glyco-bond=-- sugar=-. nts=2 GG A.G4,A.G5 strand#3 U RNA glyco-bond=-- sugar=-- nts=2 GG A.G10,A.G11 strand#4 U RNA glyco-bond=-- sugar=-- nts=2 GG A.G13,A.G14 loop#1 type=propeller strands=[#1,#2] nts=1 A A.A3 loop#2 type=propeller strands=[#2,#3] nts=4 UUUU A.U6,A.U7,A.U8,A.U9 loop#3 type=propeller strands=[#3,#4] nts=1 A A.A12 |
Stem#2, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.G15,B.G18,B.G24,B.G27 2 glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG B.G16,B.G19,B.G25,B.G28 step#1 pm(>>,forward) area=9.00 rise=4.04 twist=32.8 strand#1 U RNA glyco-bond=-- sugar=-- nts=2 GG B.G15,B.G16 strand#2 U RNA glyco-bond=-- sugar=-3 nts=2 GG B.G18,B.G19 strand#3 U RNA glyco-bond=-- sugar=-- nts=2 GG B.G24,B.G25 strand#4 U RNA glyco-bond=-- sugar=-- nts=2 GG B.G27,B.G28 loop#1 type=propeller strands=[#1,#2] nts=1 A B.A17 loop#2 type=propeller strands=[#2,#3] nts=4 UUUU B.U20,B.U21,B.U22,B.U23 loop#3 type=propeller strands=[#3,#4] nts=1 A B.A26 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5']