Summary information and primary citation

PDB-id
1d59
Class
DNA
Method
X-ray (2.3 Å)
Summary
Crystal structure of 4-stranded oxytricha telomeric DNA
Reference
Kang C, Zhang X, Ratliff R, Moyzis R, Rich A (1992): "Crystal structure of four-stranded Oxytricha telomeric DNA." Nature, 356, 126-131. doi: 10.1038/356126a0.
Abstract
The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, UDUD, anti-parallel:chair, 2+2

Cartoon-block schematics in six views (download the tarball)

PyMOL session file

Download PDB file

View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=--s- sugar=-.-- groove=-wn- planarity=0.244 type=other  -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:B.DG21,1:A.DG12
 2 glyco-bond=-s-s sugar=33-. groove=wnwn planarity=0.284 type=other  -- nts=4 GGGG 1:A.DG2,1:A.DG11,1:B.DG22,1:B.DG15
 3 glyco-bond=--s- sugar=3-3- groove=-wn- planarity=0.425 type=other  -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:B.DG23,1:A.DG10
 4 glyco-bond=-s-s sugar=-33. groove=wnwn planarity=0.374 type=other  -- nts=4 GGGG 1:A.DG4,1:A.DG9,1:B.DG24,1:B.DG13

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, 4 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=--s- sugar=-.-- groove=-wn- WC-->Major -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:B.DG21,1:A.DG12
 2  glyco-bond=-s-s sugar=3.-3 groove=nwnw Major-->WC -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:B.DG22,1:A.DG11
 3  glyco-bond=--s- sugar=3-3- groove=-wn- WC-->Major -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:B.DG23,1:A.DG10
 4  glyco-bond=-s-s sugar=-.33 groove=nwnw Major-->WC -- nts=4 GGGG 1:A.DG4,1:B.DG13,1:B.DG24,1:A.DG9
  step#1  mm(<>,outward)  area=9.62  rise=3.46 twist=28.8
  step#2  pp(><,inward)   area=25.87 rise=3.47 twist=28.0
  step#3  mm(<>,outward)  area=16.06 rise=3.48 twist=32.3
  strand#1 DNA glyco-bond=---- sugar=-33- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4
  strand#2 DNA glyco-bond=-s-s sugar=..-. nts=4 GGGG 1:B.DG16,1:B.DG15,1:B.DG14,1:B.DG13
  strand#3 DNA glyco-bond=s-s- sugar=--33 nts=4 GGGG 1:B.DG21,1:B.DG22,1:B.DG23,1:B.DG24
  strand#4 DNA glyco-bond=-s-s sugar=-3-3 nts=4 GGGG 1:A.DG12,1:A.DG11,1:A.DG10,1:A.DG9

Download PDB file
Interactive view in 3Dmol.js
3 stacking diagrams 
 1  glyco-bond=--s- sugar=-.-- groove=-wn- WC-->Major -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:B.DG21,1:A.DG12
 2  glyco-bond=-s-s sugar=3.-3 groove=nwnw Major-->WC -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:B.DG22,1:A.DG11
  step#1  mm(<>,outward)  area=9.62  rise=3.46 twist=28.8

Download PDB file
Interactive view in 3Dmol.js

 
 2  glyco-bond=-s-s sugar=3.-3 groove=nwnw Major-->WC -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:B.DG22,1:A.DG11
 3  glyco-bond=--s- sugar=3-3- groove=-wn- WC-->Major -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:B.DG23,1:A.DG10
  step#2  pp(><,inward)   area=25.87 rise=3.47 twist=28.0

Download PDB file
Interactive view in 3Dmol.js

 
 3  glyco-bond=--s- sugar=3-3- groove=-wn- WC-->Major -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:B.DG23,1:A.DG10
 4  glyco-bond=-s-s sugar=-.33 groove=nwnw Major-->WC -- nts=4 GGGG 1:A.DG4,1:B.DG13,1:B.DG24,1:A.DG9
  step#3  mm(<>,outward)  area=16.06 rise=3.48 twist=32.3

Download PDB file
Interactive view in 3Dmol.js

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, 4 G-tetrads, 2 loops, inter-molecular, UDUD, anti-parallel:chair, WARNING, 2+2, WARNING
 1  glyco-bond=--s- sugar=---. groove=-nw- Major-->WC -- nts=4 GGGG 1:A.DG1,1:A.DG12,1:B.DG21,1:B.DG16
 2  glyco-bond=-s-s sugar=33-. groove=wnwn WC-->Major -- nts=4 GGGG 1:A.DG2,1:A.DG11,1:B.DG22,1:B.DG15
 3  glyco-bond=--s- sugar=3-3- groove=-nw- Major-->WC -- nts=4 GGGG 1:A.DG3,1:A.DG10,1:B.DG23,1:B.DG14
 4  glyco-bond=-s-s sugar=-33. groove=wnwn WC-->Major -- nts=4 GGGG 1:A.DG4,1:A.DG9,1:B.DG24,1:B.DG13
  step#1  mm(<>,outward)  area=9.62  rise=3.46 twist=28.8
  step#2  pp(><,inward)   area=25.87 rise=3.47 twist=28.0
  step#3  mm(<>,outward)  area=16.06 rise=3.48 twist=32.3
  strand#1  U DNA glyco-bond=---- sugar=-33- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4
  strand#2  D DNA glyco-bond=-s-s sugar=-3-3 nts=4 GGGG 1:A.DG12,1:A.DG11,1:A.DG10,1:A.DG9
  strand#3  U DNA glyco-bond=s-s- sugar=--33 nts=4 GGGG 1:B.DG21,1:B.DG22,1:B.DG23,1:B.DG24
  strand#4  D DNA glyco-bond=-s-s sugar=..-. nts=4 GGGG 1:B.DG16,1:B.DG15,1:B.DG14,1:B.DG13
  loop#1 type=lateral   strands=[#1,#2] nts=4 TTTT 1:A.DT5,1:A.DT6,1:A.DT7,1:A.DT8
  loop#2 type=lateral   strands=[#4,#3] nts=4 TTTT 1:B.DT17,1:B.DT18,1:B.DT19,1:B.DT20

Download PDB file
Interactive view in 3Dmol.js