DSSR-enabled G4 identification/annotation: PDB entry 4u92
Summary information and primary citation
- PDB-id
- 4u92
- Class
- DNA
- Method
- X-ray (1.5 Å)
- Summary
- Crystal structure of a DNA-ba2+ g-quadruplex containing a water-mediated c-tetrad
- Reference
- Zhang D, Huang T, Lukeman PS, Paukstelis PJ (2014): "Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad." Nucleic Acids Res., 42, 13422-13429. doi: 10.1093/nar/gku1122.
- Abstract
- We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation.
- G4 notes
- 8 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, coaxial interfaces: 3'/3'
Cartoon-block schematics in six views (download the tarball)
List of 8 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.105 type=planar -- nts=4 GGGG 1:A.DG5,4:A.DG5,2:A.DG5,3:A.DG5 2 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=bowl -- nts=4 GGGG 1:A.DG7,4:A.DG7,2:A.DG7,3:A.DG7 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.256 type=other -- nts=4 GGGG 1:A.DG9,4:A.DG9,2:A.DG9,3:A.DG9 4 glyco-bond=---- sugar=---- groove=---- planarity=0.065 type=planar -- nts=4 GGGG 1:A.DG10,4:A.DG10,2:A.DG10,3:A.DG10 5 glyco-bond=---- sugar=---- groove=---- planarity=0.085 type=planar -- nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5 6 glyco-bond=---- sugar=---- groove=---- planarity=0.217 type=bowl -- nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7 7 glyco-bond=---- sugar=3333 groove=---- planarity=0.244 type=other -- nts=4 GGGG 1:B.DG9,3:B.DG9,2:B.DG9,4:B.DG9 8 glyco-bond=---- sugar=---- groove=---- planarity=0.046 type=planar -- nts=4 GGGG 1:B.DG10,3:B.DG10,2:B.DG10,4:B.DG10
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, 8 G-tetrads, inter-molecular, with 2 stems
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,4:A.DG5,2:A.DG5,3:A.DG5 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG7,4:A.DG7,2:A.DG7,3:A.DG7 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.DG9,4:A.DG9,2:A.DG9,3:A.DG9 4* glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG10,4:A.DG10,2:A.DG10,3:A.DG10 5 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG10,3:B.DG10,2:B.DG10,4:B.DG10 6 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:B.DG9,3:B.DG9,2:B.DG9,4:B.DG9 7 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7 8 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5 step#1 pm(>>,forward) area=0.00 rise=7.07 twist=53.4 step#2 pm(>>,forward) area=13.65 rise=3.23 twist=28.7 step#3 pm(>>,forward) area=12.83 rise=3.39 twist=28.9 step#4 pp(><,inward) area=30.87 rise=3.46 twist=-160.5 step#5 mp(<<,backward) area=11.57 rise=3.44 twist=30.2 step#6 mp(<<,backward) area=14.52 rise=3.24 twist=28.3 step#7 mp(<<,backward) area=0.00 rise=7.03 twist=53.1 strand#1 DNA glyco-bond=-------- sugar=--3--3-- nts=8 GGGGGGGG 1:A.DG5,1:A.DG7,1:A.DG9,1:A.DG10,1:B.DG10,1:B.DG9,1:B.DG7,1:B.DG5 strand#2 DNA glyco-bond=-------- sugar=--3--3-- nts=8 GGGGGGGG 4:A.DG5,4:A.DG7,4:A.DG9,4:A.DG10,3:B.DG10,3:B.DG9,3:B.DG7,3:B.DG5 strand#3 DNA glyco-bond=-------- sugar=--3--3-- nts=8 GGGGGGGG 2:A.DG5,2:A.DG7,2:A.DG9,2:A.DG10,2:B.DG10,2:B.DG9,2:B.DG7,2:B.DG5 strand#4 DNA glyco-bond=-------- sugar=--3--3-- nts=8 GGGGGGGG 3:A.DG5,3:A.DG7,3:A.DG9,3:A.DG10,4:B.DG10,4:B.DG9,4:B.DG7,4:B.DG5 |
| 7 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,4:A.DG5,2:A.DG5,3:A.DG5 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG7,4:A.DG7,2:A.DG7,3:A.DG7 |
|
3 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.DG9,4:A.DG9,2:A.DG9,3:A.DG9 |
|
4* glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG10,4:A.DG10,2:A.DG10,3:A.DG10 |
|
5 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG10,3:B.DG10,2:B.DG10,4:B.DG10 |
|
6 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:B.DG9,3:B.DG9,2:B.DG9,4:B.DG9 |
|
7 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7 |
List of 2 G4-stems
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, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,4:A.DG5,2:A.DG5,3:A.DG5 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG7,4:A.DG7,2:A.DG7,3:A.DG7 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.DG9,4:A.DG9,2:A.DG9,3:A.DG9 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG10,4:A.DG10,2:A.DG10,3:A.DG10 step#1 pm(>>,forward) area=0.00 rise=7.07 twist=53.4 step#2 pm(>>,forward) area=13.65 rise=3.23 twist=28.7 step#3 pm(>>,forward) area=12.83 rise=3.39 twist=28.9 strand#1* U DNA glyco-bond=---- sugar=--3- nts=4 GGGG 1:A.DG5,1:A.DG7,1:A.DG9,1:A.DG10 bulged-nts=2 CT 1:A.DC6,1:A.DT8 strand#2* U DNA glyco-bond=---- sugar=--3- nts=4 GGGG 4:A.DG5,4:A.DG7,4:A.DG9,4:A.DG10 bulged-nts=2 CT 4:A.DC6,4:A.DT8 strand#3* U DNA glyco-bond=---- sugar=--3- nts=4 GGGG 2:A.DG5,2:A.DG7,2:A.DG9,2:A.DG10 bulged-nts=2 CT 2:A.DC6,2:A.DT8 strand#4* U DNA glyco-bond=---- sugar=--3- nts=4 GGGG 3:A.DG5,3:A.DG7,3:A.DG9,3:A.DG10 bulged-nts=2 CT 3:A.DC6,3:A.DT8 |
Stem#2, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:B.DG9,3:B.DG9,2:B.DG9,4:B.DG9 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG10,3:B.DG10,2:B.DG10,4:B.DG10 step#1 pm(>>,forward) area=0.00 rise=7.03 twist=53.1 step#2 pm(>>,forward) area=14.52 rise=3.24 twist=28.3 step#3 pm(>>,forward) area=11.57 rise=3.44 twist=30.2 strand#1* U DNA glyco-bond=---- sugar=--3- nts=4 GGGG 1:B.DG5,1:B.DG7,1:B.DG9,1:B.DG10 bulged-nts=2 CT 1:B.DC6,1:B.DT8 strand#2* U DNA glyco-bond=---- sugar=--3- nts=4 GGGG 3:B.DG5,3:B.DG7,3:B.DG9,3:B.DG10 bulged-nts=2 CT 3:B.DC6,3:B.DT8 strand#3* U DNA glyco-bond=---- sugar=--3- nts=4 GGGG 2:B.DG5,2:B.DG7,2:B.DG9,2:B.DG10 bulged-nts=2 CT 2:B.DC6,2:B.DT8 strand#4* U DNA glyco-bond=---- sugar=--3- nts=4 GGGG 4:B.DG5,4:B.DG7,4:B.DG9,4:B.DG10 bulged-nts=2 CT 4:B.DC6,4:B.DT8 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [3'/3']