Summary information

PDB id
1jb7
Class
DNA-binding protein-DNA
Method
X-ray (1.86 Å)
Summary
DNA g-quartets in a 1.86 Å resolution structure of an oxytricha nova telomeric protein-DNA complex
Reference
Horvath MP, Schultz SC (2001): "DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex." J.Mol.Biol., 310, 367-377. doi: 10.1006/jmbi.2001.4766.
Abstract
The Oxytricha nova telomere end binding protein (OnTEBP) recognizes, binds and protects the single-stranded 3'-terminal DNA extension found at the ends of macronuclear chromosomes. The structure of this complex shows that the single strand GGGGTTTTGGGG DNA binds in a deep cleft between the two protein subunits of OnTEBP, adopting a non-helical and irregular conformation. In extending the resolution limit of this structure to 1.86 A, we were surprised to find a G-quartet linked dimer of the GGGGTTTTGGGG DNA also packing within the crystal lattice and interacting with the telomere end binding protein. The G-quartet DNA exhibits the same structure and topology as previously observed in solution by NMR with diagonally crossing d(TTTT) loops at either end of the four-stranded helix. Additionally, the crystal structure reveals clearly visible Na(+), and specific patterns of bound water molecules in the four non-equivalent grooves. Although the G-quartet:protein contact surfaces are modest and might simply represent crystal packing interactions, it is interesting to speculate that the two types of telomeric DNA-protein interactions observed here might both be important in telomere biology.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UDDU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.321 type=bowl   nts=4 GGGG G.DG1,H.DG4,G.DG12,H.DG9
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.168 type=other  nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.157 type=planar nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.287 type=bowl   nts=4 GGGG G.DG4,H.DG1,G.DG9,H.DG12

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-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG1,H.DG4,G.DG12,H.DG9
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG4,H.DG1,G.DG9,H.DG12
  step#1  mm(<>,outward)  area=14.24 rise=3.41 twist=17.4
  step#2  pp(><,inward)   area=15.56 rise=3.54 twist=35.5
  step#3  mm(<>,outward)  area=14.73 rise=3.39 twist=17.8
  strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG G.DG1,G.DG2,G.DG3,G.DG4
  strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG H.DG4,H.DG3,H.DG2,H.DG1
  strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG G.DG12,G.DG11,G.DG10,G.DG9
  strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG H.DG9,H.DG10,H.DG11,H.DG12

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3 stacking diagrams 
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG1,H.DG4,G.DG12,H.DG9
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
  step#1  mm(<>,outward)  area=14.24 rise=3.41 twist=17.4

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 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
  step#2  pp(><,inward)   area=15.56 rise=3.54 twist=35.5

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 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG4,H.DG1,G.DG9,H.DG12
  step#3  mm(<>,outward)  area=14.73 rise=3.39 twist=17.8

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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, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG1,H.DG4,G.DG12,H.DG9
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG4,H.DG1,G.DG9,H.DG12
  step#1  mm(<>,outward)  area=14.24 rise=3.41 twist=17.4
  step#2  pp(><,inward)   area=15.56 rise=3.54 twist=35.5
  step#3  mm(<>,outward)  area=14.73 rise=3.39 twist=17.8
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG G.DG1,G.DG2,G.DG3,G.DG4
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG H.DG4,H.DG3,H.DG2,H.DG1
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG G.DG12,G.DG11,G.DG10,G.DG9
  strand#4  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG H.DG9,H.DG10,H.DG11,H.DG12
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT G.DT5,G.DT6,G.DT7,G.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT H.DT5,H.DT6,H.DT7,H.DT8

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