Detailed DSSR results for the G-quadruplex: PDB entry 4xk0
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
- 4xk0
- Class
- RNA
- Method
- X-ray (1.08 Å)
- Summary
- Crystal structure of a tetramolecular RNA g-quadruplex in potassium
- Reference
- Chen MC, Murat P, Abecassis K, Ferre-D'Amare AR, Balasubramanian S (2015): "Insights into the mechanism of a G-quadruplex-unwinding DEAH-box helicase." Nucleic Acids Res., 43, 2223-2231. doi: 10.1093/nar/gkv051.
- Abstract
- The unwinding of nucleic acid secondary structures within cells is crucial to maintain genomic integrity and prevent abortive transcription and translation initiation. DHX36, also known as RHAU or G4R1, is a DEAH-box ATP-dependent helicase highly specific for DNA and RNA G-quadruplexes (G4s). A fundamental mechanistic understanding of the interaction between helicases and their G4 substrates is important to elucidate G4 biology and pave the way toward G4-targeted therapies. Here we analyze how the thermodynamic stability of G4 substrates affects binding and unwinding by DHX36. We modulated the stability of the G4 substrates by varying the sequence and the number of G-tetrads and by using small, G4-stabilizing molecules. We found an inverse correlation between the thermodynamic stability of the G4 substrates and rates of unwinding by DHX36. In stark contrast, the ATPase activity of the helicase was largely independent of substrate stability pointing toward a decoupling mechanism akin to what has been observed for many double-stranded DEAD-box RNA helicases. Our study provides the first evidence that DHX36 uses a local, non-processive mechanism to unwind G4 substrates, reminiscent of that of eukaryotic initiation factor 4A (eIF4A) on double-stranded substrates.
- G4 notes
- 8 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, parallel(4+0), UUUU, coaxial interfaces: 5'/5'
Base-block schematics in six views
List of 8 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.385 type=bowl nts=4 GGGG 1:A.G1,4:A.G1,2:A.G1,3:A.G1 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.105 type=planar nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.109 type=planar nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3 4 glyco-bond=---- sugar=3333 groove=---- planarity=0.223 type=bowl nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.170 type=other nts=4 GGGG 1:C.G-2,3:C.G-2,2:C.G-2,4:C.G-2 6 glyco-bond=---- sugar=3333 groove=---- planarity=0.171 type=other nts=4 GGGG 1:C.G-1,3:C.G-1,2:C.G-1,4:C.G-1 7 glyco-bond=---- sugar=3333 groove=---- planarity=0.134 type=planar nts=4 GGGG 1:C.G0,3:C.G0,2:C.G0,4:C.G0 8 glyco-bond=---- sugar=3333 groove=---- planarity=0.246 type=bowl nts=4 GGGG 1:C.G1,3:C.G1,2:C.G1,4:C.G1
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, 8 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2 4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1,4:A.G1,2:A.G1,3:A.G1 5 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G-2,3:C.G-2,2:C.G-2,4:C.G-2 6 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G-1,3:C.G-1,2:C.G-1,4:C.G-1 7 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G0,3:C.G0,2:C.G0,4:C.G0 8 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G1,3:C.G1,2:C.G1,4:C.G1 step#1 mp(<<,backward) area=13.32 rise=3.61 twist=24.6 step#2 mp(<<,backward) area=9.01 rise=3.29 twist=33.6 step#3 mp(<<,backward) area=7.27 rise=3.20 twist=35.7 step#4 mm(<>,outward) area=25.60 rise=3.59 twist=84.4 step#5 pm(>>,forward) area=12.93 rise=3.41 twist=29.5 step#6 pm(>>,forward) area=10.90 rise=3.43 twist=30.9 step#7 pm(>>,forward) area=13.55 rise=3.68 twist=23.9 strand#1 RNA glyco-bond=-------- sugar=333-3333 nts=8 GGGGGGGG 1:A.G4,1:A.G3,1:A.G2,1:A.G1,1:C.G-2,1:C.G-1,1:C.G0,1:C.G1 strand#2 RNA glyco-bond=-------- sugar=333-3333 nts=8 GGGGGGGG 4:A.G4,4:A.G3,4:A.G2,4:A.G1,3:C.G-2,3:C.G-1,3:C.G0,3:C.G1 strand#3 RNA glyco-bond=-------- sugar=333-3333 nts=8 GGGGGGGG 2:A.G4,2:A.G3,2:A.G2,2:A.G1,2:C.G-2,2:C.G-1,2:C.G0,2:C.G1 strand#4 RNA glyco-bond=-------- sugar=333-3333 nts=8 GGGGGGGG 3:A.G4,3:A.G3,3:A.G2,3:A.G1,4:C.G-2,4:C.G-1,4:C.G0,4:C.G1 |
| 7 stacking diagrams | |
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4 |
 |
2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3 |
 |
3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2 |
 |
4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1,4:A.G1,2:A.G1,3:A.G1 |
 |
5 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G-2,3:C.G-2,2:C.G-2,4:C.G-2 |
 |
6 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G-1,3:C.G-1,2:C.G-1,4:C.G-1 |
 |
7 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G0,3:C.G0,2:C.G0,4:C.G0 |
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, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1,4:A.G1,2:A.G1,3:A.G1 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3 4 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4 step#1 pm(>>,forward) area=7.27 rise=3.20 twist=35.7 step#2 pm(>>,forward) area=9.01 rise=3.29 twist=33.6 step#3 pm(>>,forward) area=13.32 rise=3.61 twist=24.6 strand#1 U RNA glyco-bond=---- sugar=-333 nts=4 GGGG 1:A.G1,1:A.G2,1:A.G3,1:A.G4 strand#2 U RNA glyco-bond=---- sugar=-333 nts=4 GGGG 4:A.G1,4:A.G2,4:A.G3,4:A.G4 strand#3 U RNA glyco-bond=---- sugar=-333 nts=4 GGGG 2:A.G1,2:A.G2,2:A.G3,2:A.G4 strand#4 U RNA glyco-bond=---- sugar=-333 nts=4 GGGG 3:A.G1,3:A.G2,3:A.G3,3:A.G4 |
Stem#2, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G-2,3:C.G-2,2:C.G-2,4:C.G-2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G-1,3:C.G-1,2:C.G-1,4:C.G-1 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G0,3:C.G0,2:C.G0,4:C.G0 4 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:C.G1,3:C.G1,2:C.G1,4:C.G1 step#1 pm(>>,forward) area=12.93 rise=3.41 twist=29.5 step#2 pm(>>,forward) area=10.90 rise=3.43 twist=30.9 step#3 pm(>>,forward) area=13.55 rise=3.68 twist=23.9 strand#1 U RNA glyco-bond=---- sugar=3333 nts=4 GGGG 1:C.G-2,1:C.G-1,1:C.G0,1:C.G1 strand#2 U RNA glyco-bond=---- sugar=3333 nts=4 GGGG 3:C.G-2,3:C.G-1,3:C.G0,3:C.G1 strand#3 U RNA glyco-bond=---- sugar=3333 nts=4 GGGG 2:C.G-2,2:C.G-1,2:C.G0,2:C.G1 strand#4 U RNA glyco-bond=---- sugar=3333 nts=4 GGGG 4:C.G-2,4:C.G-1,4:C.G0,4:C.G1 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5']