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

PDB-id
5ew2
Class
protein-DNA
Method
X-ray (3.59 Å)
Summary
Human thrombin sandwiched between two DNA aptamers: hd22 and hd1-deltat12
Reference
Pica, A., Russo Krauss, I., Parente, V., Tateishi-Karimata, H., Nagatoishi, S., Tsumoto, K., Sugimoto, N., Sica, F.: (2017) "Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers." Nucleic Acids Res., 45, 461-469.
Abstract
Aptamers directed against human thrombin can selectively bind to two different exosites on the protein surface. The simultaneous use of two DNA aptamers, HD1 and HD22, directed to exosite I and exosite II respectively, is a very powerful approach to exploit their combined affinity. Indeed, strategies to link HD1 and HD22 together have been proposed in order to create a single bivalent molecule with an enhanced ability to control thrombin activity. In this work, the crystal structures of two ternary complexes, in which thrombin is sandwiched between two DNA aptamers, are presented and discussed. The structures shed light on the cross talk between the two exosites. The through-bond effects are particularly evident at exosite II, with net consequences on the HD22 structure. Moreover, thermodynamic data on the binding of the two aptamers are also reported and analyzed.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(+Ln+Lw+Ln), chair(2+2), UDUD

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=-s-s groove=wnwn planarity=0.756 type=bowl   nts=4 GGGG D.DG8,D.DG20,D.DG17,D.DG11
 2 glyco-bond=s-s- groove=wnwn planarity=0.637 type=bowl   nts=4 GGGG E.DG1,E.DG15,E.DG10,E.DG6
 3 glyco-bond=-s-s groove=wnwn planarity=0.543 type=other  nts=4 GGGG E.DG2,E.DG14,E.DG11,E.DG5

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

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG E.DG1,E.DG15,E.DG10,E.DG6
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG E.DG2,E.DG14,E.DG11,E.DG5
  step#1  mm(<>,outward)  area=15.01 rise=3.62 twist=14.5
  strand#1 DNA glyco-bond=s- nts=2 GG E.DG1,E.DG2
  strand#2 DNA glyco-bond=-s nts=2 GG E.DG15,E.DG14
  strand#3 DNA glyco-bond=s- nts=2 GG E.DG10,E.DG11
  strand#4 DNA glyco-bond=-s nts=2 GG E.DG6,E.DG5

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1 stacking diagram
 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG E.DG1,E.DG15,E.DG10,E.DG6
2 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG E.DG2,E.DG14,E.DG11,E.DG5
step#1 mm(<>,outward) area=15.01 rise=3.62 twist=14.5

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG E.DG1,E.DG15,E.DG10,E.DG6
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG E.DG2,E.DG14,E.DG11,E.DG5
  step#1  mm(<>,outward)  area=15.01 rise=3.62 twist=14.5
  strand#1  U DNA glyco-bond=s- nts=2 GG E.DG1,E.DG2
  strand#2  D DNA glyco-bond=-s nts=2 GG E.DG15,E.DG14
  strand#3  U DNA glyco-bond=s- nts=2 GG E.DG10,E.DG11
  strand#4  D DNA glyco-bond=-s nts=2 GG E.DG6,E.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT E.DT3,E.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TGT E.DT7,E.DG8,E.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 ?T E.3DR12,E.DT13

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

List of 3 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#-1 nts=4 GTAG D.DG8,D.DT9,D.DA10,D.DG11
 2 type=lateral   helix=#-1 nts=7 GGGCAGG D.DG11,D.DG12,D.DG13,D.DC14,D.DA15,D.DG16,D.DG17
 3 type=lateral   helix=#-1 nts=4 GTTG D.DG17,D.DT18,D.DT19,D.DG20