Summary information

PDB id
8ipp
Class
DNA binding protein-DNA
Method
X-ray (2.007 Å)
Summary
Crystal structure of the complex between an ankyrin and a parallel g-quadruplex
Reference
Ngo KH, Liew CW, Heddi B, Phan AT (2024): "Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein." J.Am.Chem.Soc., 146, 13709-13713. doi: 10.1021/jacs.4c01971.
Abstract
G-Quadruplex (G4) structures formed by guanine-rich DNA and RNA sequences are implicated in various biological processes. Understanding the mechanisms by which proteins recognize G4 structures is crucial for elucidating their functional roles. Here we present the X-ray crystal structure of an ankyrin protein bound to a parallel G4 structure. Our findings reveal a new specific recognition mode in which a bundle of α-helices and loops of the ankyrin form a flat surface to stack on the G-tetrad core. The protein employs a combination of hydrogen bonds and hydrophobic contacts to interact with the G4, and electrostatic interaction is used to enhance the binding affinity. This binding mechanism provides valuable insights into understanding G4 recognition by proteins.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=---- sugar=--.- groove=---- planarity=0.083 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.185 type=other  nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15

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

 1  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15
  step#1  pm(>>,forward)  area=10.28 rise=3.31 twist=30.0
  strand#1 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG7,A.DG8
  strand#3 DNA glyco-bond=-- sugar=.- nts=2 GG A.DG10,A.DG11
  strand#4 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG14,A.DG15

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1 stacking diagram 
 1  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15
  step#1  pm(>>,forward)  area=10.28 rise=3.31 twist=30.0

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15
  step#1  pm(>>,forward)  area=10.28 rise=3.31 twist=30.0
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG7,A.DG8
  strand#3  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG10,A.DG11
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 TG A.DT5,A.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 A A.DA9
  loop#3 type=propeller strands=[#3,#4] nts=2 TG A.DT12,A.DG13

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