DSSR-curated G4 structure: PDB entry 2m18

Summary information

PDB id: 2m18
Class: RNA
Method: NMR
Summary: Structure of stacked g-quadruplex formed by human terra sequence in potassium solution
Reference: Martadinata H, Phan AT (2013): "Structure of Human Telomeric RNA (TERRA): Stacking of Two G-Quadruplex Blocks in K(+) Solution." Biochemistry, 52, 2176-2183. doi: 10.1021/bi301606u.
Abstract: Telomeric repeat-containing RNAs (TERRA) are transcription products of the telomeres. Human TERRA sequences containing UUAGGG repeats can form parallel-stranded G-quadruplexes. The stacking interaction of such structures was shown to be important for ligand targeting and higher-order arrangement of G-quadruplexes in long TERRA sequences. Here we report on the first high-resolution structure of a stacked G-quadruplex formed by the 10-nucleotide human TERRA sequence r(GGGUUAGGGU) in potassium solution. This structure comprises two dimeric three-layer parallel-stranded G-quadruplex blocks, which stack on each other at their 5'-ends. The adenine in each UUA loop is nearly coplanar with the 5'-end G-tetrad forming an A·(G·G·G·G)·A hexad, thereby increasing the stacking contacts between the two blocks. Interestingly, this stacking and loop conformation is different from all structures previously reported for the free human TERRA but resembles the structure previously determined for a complex between a human TERRA sequence and an acridine ligand. This stacking conformation is a potential target for drugs that recognize or induce the stacking interface.
G4 notes: 6 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

PyMOL session file	PDB file	View in 3Dmol.js

List of 6 G-tetrads

 1 glyco-bond=---- sugar=3.3. groove=---- planarity=0.494 type=other  nts=4 GGGG A.G1,A.G7,B.G11,B.G17
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.419 type=saddle nts=4 GGGG A.G2,A.G8,B.G12,B.G18
 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.432 type=other  nts=4 GGGG A.G3,A.G9,B.G13,B.G19
 4 glyco-bond=---- sugar=3.3- groove=---- planarity=0.494 type=other  nts=4 GGGG C.G21,C.G27,D.G31,D.G37
 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.487 type=other  nts=4 GGGG C.G22,C.G28,D.G32,D.G38
 6 glyco-bond=---- sugar=3333 groove=---- planarity=0.498 type=other  nts=4 GGGG C.G23,C.G29,D.G33,D.G39

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=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G13,B.G19 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,A.G8,B.G12,B.G18 3* glyco-bond=---- sugar=3.3. groove=---- WC-->Major nts=4 GGGG A.G1,A.G7,B.G11,B.G17 4 glyco-bond=---- sugar=3.3- groove=---- Major-->WC nts=4 GGGG D.G31,C.G27,C.G21,D.G37 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG D.G32,C.G28,C.G22,D.G38 6 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG D.G33,C.G29,C.G23,D.G39 step#1 mp(<<,backward) area=16.77 rise=3.46 twist=28.5 step#2 mp(<<,backward) area=19.82 rise=3.76 twist=23.3 step#3 mm(<>,outward) area=9.84 rise=3.50 twist=-60.5 step#4 pm(>>,forward) area=19.75 rise=3.70 twist=23.9 step#5 pm(>>,forward) area=17.59 rise=3.48 twist=27.3 strand#1 RNA glyco-bond=------ sugar=333333 nts=6 GGGGGG A.G3,A.G2,A.G1,D.G31,D.G32,D.G33 strand#2 RNA glyco-bond=------ sugar=33..33 nts=6 GGGGGG A.G9,A.G8,A.G7,C.G27,C.G28,C.G29 strand#3 RNA glyco-bond=------ sugar=333333 nts=6 GGGGGG B.G13,B.G12,B.G11,C.G21,C.G22,C.G23 strand#4 RNA glyco-bond=------ sugar=33.-33 nts=6 GGGGGG B.G19,B.G18,B.G17,D.G37,D.G38,D.G39 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G13,B.G19 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,A.G8,B.G12,B.G18 step#1 mp(<<,backward) area=16.77 rise=3.46 twist=28.5 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,A.G8,B.G12,B.G18 3* glyco-bond=---- sugar=3.3. groove=---- WC-->Major nts=4 GGGG A.G1,A.G7,B.G11,B.G17 step#2 mp(<<,backward) area=19.82 rise=3.76 twist=23.3 Download PDB file Interactive view in 3Dmol.js
	3* glyco-bond=---- sugar=3.3. groove=---- WC-->Major nts=4 GGGG A.G1,A.G7,B.G11,B.G17 4 glyco-bond=---- sugar=3.3- groove=---- Major-->WC nts=4 GGGG D.G31,C.G27,C.G21,D.G37 step#3 mm(<>,outward) area=9.84 rise=3.50 twist=-60.5 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=3.3- groove=---- Major-->WC nts=4 GGGG D.G31,C.G27,C.G21,D.G37 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG D.G32,C.G28,C.G22,D.G38 step#4 pm(>>,forward) area=19.75 rise=3.70 twist=23.9 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG D.G32,C.G28,C.G22,D.G38 6 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG D.G33,C.G29,C.G23,D.G39 step#5 pm(>>,forward) area=17.59 rise=3.48 twist=27.3 Download PDB file Interactive view in 3Dmol.js

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-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=3.3. groove=---- WC-->Major nts=4 GGGG A.G1,A.G7,B.G11,B.G17
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,A.G8,B.G12,B.G18
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G13,B.G19
  step#1  pm(>>,forward)  area=19.82 rise=3.76 twist=23.3
  step#2  pm(>>,forward)  area=16.77 rise=3.46 twist=28.5
  strand#1  U RNA glyco-bond=--- sugar=333 nts=3 GGG A.G1,A.G2,A.G3
  strand#2  U RNA glyco-bond=--- sugar=.33 nts=3 GGG A.G7,A.G8,A.G9
  strand#3  U RNA glyco-bond=--- sugar=333 nts=3 GGG B.G11,B.G12,B.G13
  strand#4  U RNA glyco-bond=--- sugar=.33 nts=3 GGG B.G17,B.G18,B.G19
  loop#1 type=propeller strands=[#1,#2] nts=3 UUA A.U4,A.U5,A.A6
  loop#2 type=propeller strands=[#3,#4] nts=3 UUA B.U14,B.U15,B.A16

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Stem#2, 3 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=3.3- groove=---- WC-->Major nts=4 GGGG C.G21,C.G27,D.G31,D.G37
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG C.G22,C.G28,D.G32,D.G38
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG C.G23,C.G29,D.G33,D.G39
  step#1  pm(>>,forward)  area=19.75 rise=3.70 twist=23.9
  step#2  pm(>>,forward)  area=17.59 rise=3.48 twist=27.3
  strand#1  U RNA glyco-bond=--- sugar=333 nts=3 GGG C.G21,C.G22,C.G23
  strand#2  U RNA glyco-bond=--- sugar=.33 nts=3 GGG C.G27,C.G28,C.G29
  strand#3  U RNA glyco-bond=--- sugar=333 nts=3 GGG D.G31,D.G32,D.G33
  strand#4  U RNA glyco-bond=--- sugar=-33 nts=3 GGG D.G37,D.G38,D.G39
  loop#1 type=propeller strands=[#1,#2] nts=3 UUA C.U24,C.U25,C.A26
  loop#2 type=propeller strands=[#3,#4] nts=3 UUA D.U34,D.U35,D.A36