DSSR-enabled G4 identification/annotation: PDB entry 8vx8
Summary information and primary citation
- PDB-id
- 8vx8
- Class
- motor protein
- Method
- cryo-EM (3.4 Å)
- Summary
- cryo-EM structure of dhx36 bound to the cmyc DNA g-quadruplex, class 1
- Reference
- Banco MT, Paul T, Jiang J, Myong S, Ferre-D'Amare AR (2025): "Structural basis for dual DNA and RNA specificity of the G-quadruplex-resolving DEAH-box helicase DHX36." Cell Rep, 44, 116136. doi: 10.1016/j.celrep.2025.116136.
- Abstract
- DEAH-box helicases, which share a structurally conserved ATPase core, function in all facets of eukaryotic gene expression. While most helicases are highly specialized for their substrates, DHX36 (DEAH-box helicase 36) resolves both DNA and RNA G-quadruplexes. To elucidate the molecular basis of this versatility, we have determined cryo-electron microscopy structures of bovine DHX36 bound to a three-tier RNA G-quadruplex and a six-tier DNA G-quadruplex at 2.6 and 3.4 Å resolution, respectively. Kinetic and smFRET characterizations of structure-guided mutants indicate a key role for the RecA2 domain of the helicase core in DNA vs. RNA discrimination. Furthermore, our structures show that a sequence-divergent RecA2 domain surface loop synergizes with a DHX36-specific N-terminal extension to orthogonally recognize features that specify G-quadruplexes over other nucleic acid structures. Our analysis suggests that recognizing their folded substrates by DEAH-box helicases may generally involve ornamentations of their structural cores acting synergistically with specialized peripheral elements.
- G4 notes
- 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, ; UUUU, parallel, 4+0, 3(-P), coaxial interfaces: 5'/5'
Cartoon-block schematics in six views (download the tarball)
List of 6 G-tetrads
1 glyco-bond=---- sugar=---. groove=---- planarity=0.262 type=other O+ nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG15 2 glyco-bond=---- sugar=-..3 groove=---- planarity=0.207 type=other O+ nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG16 3 glyco-bond=---- sugar=---- groove=---- planarity=0.190 type=other O+ nts=4 GGGG B.DG4,B.DG8,B.DG13,B.DG17 4 glyco-bond=---- sugar=---. groove=---- planarity=0.133 type=planar O+ nts=4 GGGG C.DG2,C.DG6,C.DG11,C.DG15 5 glyco-bond=---- sugar=---3 groove=---- planarity=0.160 type=planar O+ nts=4 GGGG C.DG3,C.DG7,C.DG12,C.DG16 6 glyco-bond=---- sugar=---- groove=---- planarity=0.188 type=other O+ nts=4 GGGG C.DG4,C.DG8,C.DG13,C.DG17
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-tetrads, inter-molecular, with 2 stems
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.DG4,B.DG8,B.DG13,B.DG17 2 glyco-bond=---- sugar=-..3 groove=---- WC-->Major O+ nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG16 3* glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG15 4 glyco-bond=---- sugar=---. groove=---- Major-->WC O+ nts=4 GGGG C.DG11,C.DG6,C.DG2,C.DG15 5 glyco-bond=---- sugar=---3 groove=---- Major-->WC O+ nts=4 GGGG C.DG12,C.DG7,C.DG3,C.DG16 6 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG C.DG13,C.DG8,C.DG4,C.DG17 step#1 mp(<<,backward) area=17.00 rise=3.57 twist=21.7 step#2 mp(<<,backward) area=12.68 rise=3.23 twist=32.0 step#3 mm(<>,outward) area=18.46 rise=4.57 twist=-1.5 step#4 pm(>>,forward) area=12.93 rise=3.16 twist=32.4 step#5 pm(>>,forward) area=18.53 rise=3.26 twist=22.5 strand#1 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG B.DG4,B.DG3,B.DG2,C.DG11,C.DG12,C.DG13 strand#2 DNA glyco-bond=------ sugar=-.---- nts=6 GGGGGG B.DG8,B.DG7,B.DG6,C.DG6,C.DG7,C.DG8 strand#3 DNA glyco-bond=------ sugar=-.---- nts=6 GGGGGG B.DG13,B.DG12,B.DG11,C.DG2,C.DG3,C.DG4 strand#4 DNA glyco-bond=------ sugar=-3..3- nts=6 GGGGGG B.DG17,B.DG16,B.DG15,C.DG15,C.DG16,C.DG17 |
| 5 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.DG4,B.DG8,B.DG13,B.DG17 |
|
2 glyco-bond=---- sugar=-..3 groove=---- WC-->Major O+ nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG16 |
|
3* glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG15 |
|
4 glyco-bond=---- sugar=---. groove=---- Major-->WC O+ nts=4 GGGG C.DG11,C.DG6,C.DG2,C.DG15 |
|
5 glyco-bond=---- sugar=---3 groove=---- Major-->WC O+ nts=4 GGGG C.DG12,C.DG7,C.DG3,C.DG16 |
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, 3 G-tetrads, 0 loops, INTRA-molecular, UUUU, parallel, 4+0, descriptor
|
1 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG15 2 glyco-bond=---- sugar=-..3 groove=---- WC-->Major O+ nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG16 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.DG4,B.DG8,B.DG13,B.DG17 step#1 pm(>>,forward) area=12.68 rise=3.23 twist=32.0 step#2 pm(>>,forward) area=17.00 rise=3.57 twist=21.7 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG2,B.DG3,B.DG4 strand#2 U DNA glyco-bond=--- sugar=-.- nts=3 GGG B.DG6,B.DG7,B.DG8 strand#3 U DNA glyco-bond=--- sugar=-.- nts=3 GGG B.DG11,B.DG12,B.DG13 strand#4 U DNA glyco-bond=--- sugar=.3- nts=3 GGG B.DG15,B.DG16,B.DG17 |
Stem#2, 3 G-tetrads, 1 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P)
|
1 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG C.DG2,C.DG6,C.DG11,C.DG15 2 glyco-bond=---- sugar=---3 groove=---- WC-->Major O+ nts=4 GGGG C.DG3,C.DG7,C.DG12,C.DG16 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG C.DG4,C.DG8,C.DG13,C.DG17 step#1 pm(>>,forward) area=12.93 rise=3.16 twist=32.4 step#2 pm(>>,forward) area=18.53 rise=3.26 twist=22.5 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG2,C.DG3,C.DG4 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG6,C.DG7,C.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG11,C.DG12,C.DG13 strand#4 U DNA glyco-bond=--- sugar=.3- nts=3 GGG C.DG15,C.DG16,C.DG17 loop#1 type=propeller strands=[#3,#4] nts=1 T C.DT14 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5']