Summary information

PDB id
2jsm
Class
DNA
Method
NMR
Summary
Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two edgewise loops and double-chain reversal loop, NMR, 10 structures, form 1 natural
Reference
Phan AT, Kuryavyi V, Luu KN, Patel DJ (2007): "Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution." Nucleic Acids Res., 35, 6517-6525. doi: 10.1093/nar/gkm706.
Abstract
Intramolecular G-quadruplexes formed by human telomere sequences are attractive anticancer targets. Recently, four-repeat human telomere sequences have been shown to form two different intramolecular (3 + 1) G-quadruplexes in K(+) solution (Form 1 and Form 2). Here we report on the solution structures of both Form 1 and Form 2 adopted by natural human telomere sequences. Both structures contain the (3 + 1) G-tetrad core with one double-chain-reversal and two edgewise loops, but differ in the successive order of loop arrangements within the G-quadruplex scaffold. Our results provide the structural details at the two ends of the G-tetrad core in the context of natural sequences and information on different loop conformations. This structural information might be important for our understanding of telomere G-quadruplex structures and for anticancer drug design targeted to such scaffolds.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-Lw-Ln), hybrid-1(3+1), UUDU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=ss-s sugar=---- groove=-wn- planarity=0.124 type=planar nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21
 2 glyco-bond=--s- sugar=---3 groove=-wn- planarity=0.044 type=planar nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3 glyco-bond=--s- sugar=-.-3 groove=-wn- planarity=0.088 type=planar nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23

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, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ss-s sugar=---- groove=-wn- Major-->WC nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21
 2  glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=--s- sugar=-.-3 groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
  step#1  mm(<>,outward)  area=12.28 rise=3.34 twist=18.9
  step#2  pm(>>,forward)  area=11.09 rise=3.35 twist=29.3
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=s-- sugar=--. nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG17,A.DG16,A.DG15
  strand#4 DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG21,A.DG22,A.DG23

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2 stacking diagrams 
 1  glyco-bond=ss-s sugar=---- groove=-wn- Major-->WC nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21
 2  glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
  step#1  mm(<>,outward)  area=12.28 rise=3.34 twist=18.9

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 2  glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=--s- sugar=-.-3 groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
  step#2  pm(>>,forward)  area=11.09 rise=3.35 twist=29.3

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List of 1 G4-stem

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, 3 loops, INTRA-molecular, UUDU, hybrid-(mixed), 3(-P-Lw-Ln), hybrid-1(3+1)

 1  glyco-bond=ss-s sugar=---- groove=-wn- Major-->WC nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21
 2  glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=--s- sugar=-.-3 groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
  step#1  mm(<>,outward)  area=12.28 rise=3.34 twist=18.9
  step#2  pm(>>,forward)  area=11.09 rise=3.35 twist=29.3
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=s-- sugar=--. nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG17,A.DG16,A.DG15
  strand#4  U DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG21,A.DG22,A.DG23
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTA A.DT12,A.DT13,A.DA14
  loop#3 type=lateral   strands=[#3,#4] nts=3 TTA A.DT18,A.DT19,A.DA20

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