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

PDB-id
6q6r
Class
DNA binding protein
Method
X-ray (1.5 Å)
Summary
Recognition of different base tetrads by rhau: x-ray crystal structure of g4 recognition motif bound to the 3-end tetrad of a DNA G-quadruplex
Reference
Heddi, B., Cheong, V.V., Schmitt, E., Mechulam, Y., Phan, A.T.: (2019) "Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3'-end tetrad of a DNA G-quadruplex." J.Struct.Biol., 107399-107399.
Abstract
G-quadruplexes (G4) are secondary structures of nucleic acids that can form in cells and have diverse biological functions. Several biologically important proteins interact with G-quadruplexes, of which RHAU - a helicase from the DEAH-box superfamily, was shown to bind and unwind G-quadruplexes efficiently. We report a X-ray co-crystal structure at 1.5 Å resolution of an N-terminal fragment of RHAU bound to the exposed tetrad of a parallel-stranded G-quadruplex. The RHAU peptide folds into an L-shaped α-helix, and binds to the G-quadruplex through π-stacking and electrostatic interactions. X-ray crystal structure of our complex identified key amino acid residues important for G-quadruplex-peptide binding interaction at the 3'-end G•G•G•G tetrad. Together with previous solution and crystal structures of RHAU bound to the 5'-end G•G•G•G and G•G•A•T tetrads, our crystal structure highlights the occurrence of a robust G-quadruplex recognition motif within RHAU that can adapt to different accessible tetrads.
G4 notes
12 G-tetrads, 2 G4 helices, 4 G4 stems, 2 G4 coaxial stacks · 3(-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 12 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.084 type=planar nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
 2 glyco-bond=---- groove=---- planarity=0.129 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG14
 3 glyco-bond=---- groove=---- planarity=0.191 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 4 glyco-bond=---- groove=---- planarity=0.084 type=planar nts=4 GGGG B.DG1,B.DG5,B.DG9,B.DG13
 5 glyco-bond=---- groove=---- planarity=0.115 type=planar nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG14
 6 glyco-bond=---- groove=---- planarity=0.149 type=planar nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 7 glyco-bond=---- groove=---- planarity=0.056 type=planar nts=4 GGGG C.DG1,C.DG5,C.DG9,C.DG13
 8 glyco-bond=---- groove=---- planarity=0.108 type=planar nts=4 GGGG C.DG2,C.DG6,C.DG10,C.DG14
 9 glyco-bond=---- groove=---- planarity=0.164 type=other  nts=4 GGGG C.DG3,C.DG7,C.DG11,C.DG15
10 glyco-bond=---- groove=---- planarity=0.058 type=planar nts=4 GGGG D.DG1,D.DG5,D.DG9,D.DG13
11 glyco-bond=---- groove=---- planarity=0.089 type=planar nts=4 GGGG D.DG2,D.DG6,D.DG10,D.DG14
12 glyco-bond=---- groove=---- planarity=0.154 type=planar nts=4 GGGG D.DG3,D.DG7,D.DG11,D.DG15

List of 2 G4-helices [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, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG14
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG9,B.DG5,B.DG1,B.DG13
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG10,B.DG6,B.DG2,B.DG14
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG7,B.DG3,B.DG15
  step#1  mp(<<,backward) area=15.11 rise=3.43 twist=24.5
  step#2  mp(<<,backward) area=9.12  rise=3.34 twist=33.3
  step#3  mm(<>,outward)  area=27.99 rise=3.30 twist=-8.2
  step#4  pm(>>,forward)  area=8.83  rise=3.36 twist=34.0
  step#5  pm(>>,forward)  area=15.36 rise=3.38 twist=24.3
  strand#1 DNA glyco-bond=------ nts=6 GGGGGG A.DG3,A.DG2,A.DG1,B.DG9,B.DG10,B.DG11
  strand#2 DNA glyco-bond=------ nts=6 GGGGGG A.DG7,A.DG6,A.DG5,B.DG5,B.DG6,B.DG7
  strand#3 DNA glyco-bond=------ nts=6 GGGGGG A.DG11,A.DG10,A.DG9,B.DG1,B.DG2,B.DG3
  strand#4 DNA glyco-bond=------ nts=6 GGGGGG A.DG15,A.DG14,A.DG13,B.DG13,B.DG14,B.DG15

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG14
step#1 mp(<<,backward) area=15.11 rise=3.43 twist=24.5

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG14
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
step#2 mp(<<,backward) area=9.12 rise=3.34 twist=33.3

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 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG9,B.DG5,B.DG1,B.DG13
step#3 mm(<>,outward) area=27.99 rise=3.30 twist=-8.2

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG9,B.DG5,B.DG1,B.DG13
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG10,B.DG6,B.DG2,B.DG14
step#4 pm(>>,forward) area=8.83 rise=3.36 twist=34.0

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG10,B.DG6,B.DG2,B.DG14
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG7,B.DG3,B.DG15
step#5 pm(>>,forward) area=15.36 rise=3.38 twist=24.3

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Helix#2, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,C.DG11,C.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG6,C.DG10,C.DG14
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG1,C.DG5,C.DG9,C.DG13
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.DG9,D.DG5,D.DG1,D.DG13
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.DG10,D.DG6,D.DG2,D.DG14
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.DG11,D.DG7,D.DG3,D.DG15
  step#1  mp(<<,backward) area=14.45 rise=3.40 twist=25.3
  step#2  mp(<<,backward) area=9.02  rise=3.35 twist=33.2
  step#3  mm(<>,outward)  area=27.92 rise=3.29 twist=-8.4
  step#4  pm(>>,forward)  area=8.37  rise=3.35 twist=34.3
  step#5  pm(>>,forward)  area=15.64 rise=3.40 twist=23.9
  strand#1 DNA glyco-bond=------ nts=6 GGGGGG C.DG3,C.DG2,C.DG1,D.DG9,D.DG10,D.DG11
  strand#2 DNA glyco-bond=------ nts=6 GGGGGG C.DG7,C.DG6,C.DG5,D.DG5,D.DG6,D.DG7
  strand#3 DNA glyco-bond=------ nts=6 GGGGGG C.DG11,C.DG10,C.DG9,D.DG1,D.DG2,D.DG3
  strand#4 DNA glyco-bond=------ nts=6 GGGGGG C.DG15,C.DG14,C.DG13,D.DG13,D.DG14,D.DG15

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,C.DG11,C.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG6,C.DG10,C.DG14
step#1 mp(<<,backward) area=14.45 rise=3.40 twist=25.3

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG6,C.DG10,C.DG14
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG1,C.DG5,C.DG9,C.DG13
step#2 mp(<<,backward) area=9.02 rise=3.35 twist=33.2

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 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG1,C.DG5,C.DG9,C.DG13
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.DG9,D.DG5,D.DG1,D.DG13
step#3 mm(<>,outward) area=27.92 rise=3.29 twist=-8.4

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.DG9,D.DG5,D.DG1,D.DG13
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.DG10,D.DG6,D.DG2,D.DG14
step#4 pm(>>,forward) area=8.37 rise=3.35 twist=34.3

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.DG10,D.DG6,D.DG2,D.DG14
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.DG11,D.DG7,D.DG3,D.DG15
step#5 pm(>>,forward) area=15.64 rise=3.40 twist=23.9

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List of 4 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, 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 A.DG1,A.DG5,A.DG9,A.DG13
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
  step#1  pm(>>,forward)  area=9.12  rise=3.34 twist=33.3
  step#2  pm(>>,forward)  area=15.11 rise=3.43 twist=24.5
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG5,A.DG6,A.DG7
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT4
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT8
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT12

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Stem#2, 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.DG1,B.DG5,B.DG9,B.DG13
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
  step#1  pm(>>,forward)  area=8.83  rise=3.36 twist=34.0
  step#2  pm(>>,forward)  area=15.36 rise=3.38 twist=24.3
  strand#1  U DNA glyco-bond=--- nts=3 GGG B.DG1,B.DG2,B.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG5,B.DG6,B.DG7
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG9,B.DG10,B.DG11
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG13,B.DG14,B.DG15
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT4
  loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT8
  loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT12

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Stem#3, 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 C.DG1,C.DG5,C.DG9,C.DG13
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG6,C.DG10,C.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,C.DG11,C.DG15
  step#1  pm(>>,forward)  area=9.02  rise=3.35 twist=33.2
  step#2  pm(>>,forward)  area=14.45 rise=3.40 twist=25.3
  strand#1  U DNA glyco-bond=--- nts=3 GGG C.DG1,C.DG2,C.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG C.DG5,C.DG6,C.DG7
  strand#3  U DNA glyco-bond=--- nts=3 GGG C.DG9,C.DG10,C.DG11
  strand#4  U DNA glyco-bond=--- nts=3 GGG C.DG13,C.DG14,C.DG15
  loop#1 type=propeller strands=[#1,#2] nts=1 T C.DT4
  loop#2 type=propeller strands=[#2,#3] nts=1 T C.DT8
  loop#3 type=propeller strands=[#3,#4] nts=1 T C.DT12

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Stem#4, 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 D.DG1,D.DG5,D.DG9,D.DG13
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG D.DG2,D.DG6,D.DG10,D.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG D.DG3,D.DG7,D.DG11,D.DG15
  step#1  pm(>>,forward)  area=8.37  rise=3.35 twist=34.3
  step#2  pm(>>,forward)  area=15.64 rise=3.40 twist=23.9
  strand#1  U DNA glyco-bond=--- nts=3 GGG D.DG1,D.DG2,D.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG D.DG5,D.DG6,D.DG7
  strand#3  U DNA glyco-bond=--- nts=3 GGG D.DG9,D.DG10,D.DG11
  strand#4  U DNA glyco-bond=--- nts=3 GGG D.DG13,D.DG14,D.DG15
  loop#1 type=propeller strands=[#1,#2] nts=1 T D.DT4
  loop#2 type=propeller strands=[#2,#3] nts=1 T D.DT8
  loop#3 type=propeller strands=[#3,#4] nts=1 T D.DT12

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List of 2 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']
 2 G4 helix#2 contains 2 G4 stems: [#3,#4]  [5'/5']

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