Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
6ldm
Class
DNA binding protein-DNA
Method
X-ray (2.4 Å)
Summary
Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein rap1
Reference
Traczyk, A., Liew, C.W., Gill, D.J., Rhodes, D.: (2020) "Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1." Nucleic Acids Res., 48, 4562-4571.
Abstract
G-quadruplexes are four-stranded nucleic acid structures involved in multiple cellular pathways including DNA replication and telomere maintenance. Such structures are formed by G-rich DNA sequences typified by telomeric DNA repeats. Whilst there is evidence for proteins that bind and regulate G-quadruplex formation, the molecular basis for this remains poorly understood. The budding yeast telomeric protein Rap1, originally identified as a transcriptional regulator functioning by recognizing double-stranded DNA binding sites, was one of the first proteins to be discovered to also bind and promote G-quadruplex formation in vitro. Here, we present the 2.4 Å resolution crystal structure of the Rap1 DNA-binding domain in complex with a G-quadruplex. Our structure not only provides a detailed insight into the structural basis for G-quadruplex recognition by a protein, but also gives a mechanistic understanding of how the same DNA-binding domain adapts to specifically recognize different DNA structures. The key observation is the DNA-recognition helix functions in a bimodal manner: In double-stranded DNA recognition one helix face makes electrostatic interactions with the major groove of DNA, whereas in G-quadruplex recognition a different helix face is used to make primarily hydrophobic interactions with the planar face of a G-tetrad.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.078 type=planar nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2 glyco-bond=---- groove=---- planarity=0.155 type=planar nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3 glyco-bond=---- groove=---- planarity=0.225 type=bowl   nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
  step#1  pm(>>,forward)  area=12.85 rise=3.39 twist=29.3
  step#2  pm(>>,forward)  area=9.07  rise=3.37 twist=30.3
  strand#1 DNA glyco-bond=--- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#2 DNA glyco-bond=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#3 DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4 DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
step#1 pm(>>,forward) area=12.85 rise=3.39 twist=29.3

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
step#2 pm(>>,forward) area=9.07 rise=3.37 twist=30.3

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
  step#1  pm(>>,forward)  area=12.85 rise=3.39 twist=29.3
  step#2  pm(>>,forward)  area=9.07  rise=3.37 twist=30.3
  strand#1  U DNA glyco-bond=--- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT6
  loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT10
  loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT14

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)