Detailed DSSR results for the G-quadruplex: PDB entry 2mb4
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 2mb4
- Class
- DNA
- Method
- NMR
- Summary
- Solution structure of a stacked dimeric g-quadruplex formed by a segment of the human ceb1 minisatellite
- Reference
- Adrian M, Ang DJ, Lech CJ, Heddi B, Nicolas A, Phan AT (2014): "Structure and Conformational Dynamics of a Stacked Dimeric G-Quadruplex Formed by the Human CEB1 Minisatellite." J.Am.Chem.Soc., 136, 6297-6305. doi: 10.1021/ja4125274.
- Abstract
- CEB1 is a highly polymorphic human minisatellite. In yeast, the size variation of CEB1 tandem arrays has been associated with the capacity of the motif to form G-quadruplexes. Here we report on the NMR solution structure of a G-quadruplex formed by the CEB1 DNA G-rich fragment d(AGGGGGGAGGGAGGGTGG), harboring several G-tracts including one with six continuous guanines. This sequence forms a dimeric G-quadruplex involving the stacking of two subunits, each being a unique snapback parallel-stranded scaffold with three G-tetrad layers, three double-chain-reversal loops, and a V-shaped loop. The two subunits are stacked at their 5'-end tetrads, and multiple stacking rotamers may be present due to a high symmetry at the stacking interface. There is a conformational exchange in the millisecond time scale involving a swapping motion between two bases of the six-guanine tract. Our results not only add to the understanding of how the G-quadruplex formation in human minisatellite leads to genetic instability but also address the fundamental questions regarding stacking of G-quadruplexes and how a long continuous G-tract participates in the structure and conformational dynamics of G-quadruplexes.
- G4 notes
- 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, 2(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'
Base-block schematics in six views
List of 6 G-tetrads
1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.198 type=other nts=4 GGGG A.DG3,A.DG15,A.DG11,A.DG7 2 glyco-bond=---- sugar=---- groove=---- planarity=0.106 type=planar nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17 3 glyco-bond=---- sugar=-.-- groove=---- planarity=0.141 type=planar nts=4 GGGG A.DG6,A.DG10,A.DG14,A.DG18 4 glyco-bond=s--- sugar=---. groove=w--n planarity=0.163 type=other nts=4 GGGG B.DG3,B.DG15,B.DG11,B.DG7 5 glyco-bond=---- sugar=---- groove=---- planarity=0.155 type=planar nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17 6 glyco-bond=---- sugar=---- groove=---- planarity=0.143 type=planar nts=4 GGGG B.DG6,B.DG10,B.DG14,B.DG18
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, 6 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG3,A.DG15,A.DG11,A.DG7 2 glyco-bond=---- sugar=--.- groove=---- Major-->WC nts=4 GGGG A.DG18,A.DG14,A.DG10,A.DG6 3* glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG17,A.DG13,A.DG9,A.DG5 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG9,B.DG13,B.DG17,B.DG5 5 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG10,B.DG14,B.DG18,B.DG6 6 glyco-bond=--s- sugar=---. groove=-wn- WC-->Major nts=4 GGGG B.DG11,B.DG15,B.DG3,B.DG7 step#1 mp(<<,backward) area=11.51 rise=3.53 twist=30.0 step#2 mp(<<,backward) area=9.04 rise=3.25 twist=31.4 step#3 mm(<>,outward) area=26.59 rise=3.55 twist=-8.7 step#4 pm(>>,forward) area=12.09 rise=3.38 twist=29.8 step#5 pm(>>,forward) area=9.65 rise=3.25 twist=31.3 strand#1 DNA glyco-bond=s----- sugar=------ nts=6 GGGGGG A.DG3,A.DG18,A.DG17,B.DG9,B.DG10,B.DG11 strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG15,A.DG14,A.DG13,B.DG13,B.DG14,B.DG15 strand#3 DNA glyco-bond=-----s sugar=-.---- nts=6 GGGGGG A.DG11,A.DG10,A.DG9,B.DG17,B.DG18,B.DG3 strand#4 DNA glyco-bond=------ sugar=-----. nts=6 GGGGGG A.DG7,A.DG6,A.DG5,B.DG5,B.DG6,B.DG7 |
| 5 stacking diagrams | |
 |
1 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG3,A.DG15,A.DG11,A.DG7 |
 |
2 glyco-bond=---- sugar=--.- groove=---- Major-->WC nts=4 GGGG A.DG18,A.DG14,A.DG10,A.DG6 |
 |
3* glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG17,A.DG13,A.DG9,A.DG5 |
 |
4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG9,B.DG13,B.DG17,B.DG5 |
 |
5 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG10,B.DG14,B.DG18,B.DG6 |
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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17 2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG14,A.DG18 step#1 pm(>>,forward) area=9.04 rise=3.25 twist=31.4 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG5,A.DG6 strand#2 U DNA glyco-bond=-- sugar=-. nts=2 GG A.DG9,A.DG10 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG13,A.DG14 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG17,A.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 GA A.DG7,A.DA8 loop#2 type=propeller strands=[#2,#3] nts=2 GA A.DG11,A.DA12 loop#3 type=propeller strands=[#3,#4] nts=2 GT A.DG15,A.DT16 |
Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG6,B.DG10,B.DG14,B.DG18 step#1 pm(>>,forward) area=12.09 rise=3.38 twist=29.8 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG5,B.DG6 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG9,B.DG10 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG13,B.DG14 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG17,B.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 GA B.DG7,B.DA8 loop#2 type=propeller strands=[#2,#3] nts=2 GA B.DG11,B.DA12 loop#3 type=propeller strands=[#3,#4] nts=2 GT B.DG15,B.DT16 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5']
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=5 GGGGG A.DG3,A.DG4,A.DG5,A.DG6,A.DG7 2 type=V-shaped helix=#1 nts=5 GGGGG B.DG3,B.DG4,B.DG5,B.DG6,B.DG7