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

PDB-id
2ru7
Class
membrane protein-RNA
Method
NMR
Summary
Refined structure of RNA aptamer in complex with the partial binding peptide of prion protein
Reference
Hayashi, T., Oshima, H., Mashima, T., Nagata, T., Katahira, M., Kinoshita, M.: (2014) "Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition." Nucleic Acids Res.
Abstract
It is a central issue to elucidate the new type of molecular recognition accompanied by a global structural change of a molecule upon binding to its targets. Here we investigate the driving force for the binding of R12 (a ribonucleic acid aptamer) and P16 (a partial peptide of a prion protein) during which P16 exhibits the global structural change. We calculate changes in thermodynamic quantities upon the R12-P16 binding using a statistical-mechanical approach combined with molecular models for water which is currently best suited to studies on hydration of biomolecules. The binding is driven by a water-entropy gain originating primarily from an increase in the total volume available to the translational displacement of water molecules in the system. The energy decrease due to the gain of R12-P16 attractive (van der Waals and electrostatic) interactions is almost canceled out by the energy increase related to the loss of R12-water and P16-water attractive interactions. We can explain the general experimental result that stacking of flat moieties, hydrogen bonding and molecular-shape and electrostatic complementarities are frequently observed in the complexes. It is argued that the water-entropy gain is largely influenced by the geometric characteristics (overall shapes, sizes and detailed polyatomic structures) of the biomolecules.
G4 notes
4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · 2(-P-P-P), parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.218 type=other  nts=4 GGGG A.G1,A.G4,A.G7,A.G10
 2 glyco-bond=---- groove=---- planarity=0.312 type=bowl   nts=4 GGGG A.G2,A.G5,A.G8,A.G11
 3 glyco-bond=---- groove=---- planarity=0.225 type=other  nts=4 GGGG B.G13,B.G16,B.G19,B.G22
 4 glyco-bond=---- groove=---- planarity=0.341 type=bowl   nts=4 GGGG B.G14,B.G17,B.G20,B.G23

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, 4 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G5,A.G8,A.G11
 2* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G1,A.G4,A.G7,A.G10
 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G16,B.G13,B.G22,B.G19
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G17,B.G14,B.G23,B.G20
  step#1  mp(<<,backward) area=12.01 rise=3.32 twist=31.3
  step#2  mm(<>,outward)  area=22.82 rise=3.46 twist=6.7
  step#3  pm(>>,forward)  area=11.28 rise=3.40 twist=29.2
  strand#1 RNA glyco-bond=---- nts=4 GGGG A.G2,A.G1,B.G16,B.G17
  strand#2 RNA glyco-bond=---- nts=4 GGGG A.G5,A.G4,B.G13,B.G14
  strand#3 RNA glyco-bond=---- nts=4 GGGG A.G8,A.G7,B.G22,B.G23
  strand#4 RNA glyco-bond=---- nts=4 GGGG A.G11,A.G10,B.G19,B.G20

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G5,A.G8,A.G11
2* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G1,A.G4,A.G7,A.G10
step#1 mp(<<,backward) area=12.01 rise=3.32 twist=31.3

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 2* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G1,A.G4,A.G7,A.G10
3 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G16,B.G13,B.G22,B.G19
step#2 mm(<>,outward) area=22.82 rise=3.46 twist=6.7

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 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G16,B.G13,B.G22,B.G19
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G17,B.G14,B.G23,B.G20
step#3 pm(>>,forward) area=11.28 rise=3.40 twist=29.2

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List of 2 G4-stems [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, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G1,A.G4,A.G7,A.G10
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G5,A.G8,A.G11
  step#1  pm(>>,forward)  area=12.01 rise=3.32 twist=31.3
  strand#1  U RNA glyco-bond=-- nts=2 GG A.G1,A.G2
  strand#2  U RNA glyco-bond=-- nts=2 GG A.G4,A.G5
  strand#3  U RNA glyco-bond=-- nts=2 GG A.G7,A.G8
  strand#4  U RNA glyco-bond=-- nts=2 GG A.G10,A.G11
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.A3
  loop#2 type=propeller strands=[#2,#3] nts=1 A A.A6
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.A9

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G13,B.G16,B.G19,B.G22
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G14,B.G17,B.G20,B.G23
  step#1  pm(>>,forward)  area=11.28 rise=3.40 twist=29.2
  strand#1  U RNA glyco-bond=-- nts=2 GG B.G13,B.G14
  strand#2  U RNA glyco-bond=-- nts=2 GG B.G16,B.G17
  strand#3  U RNA glyco-bond=-- nts=2 GG B.G19,B.G20
  strand#4  U RNA glyco-bond=-- nts=2 GG B.G22,B.G23
  loop#1 type=propeller strands=[#1,#2] nts=1 A B.A15
  loop#2 type=propeller strands=[#2,#3] nts=1 A B.A18
  loop#3 type=propeller strands=[#3,#4] nts=1 A B.A21

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']

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