DSSR-enabled G4 identification/annotation: PDB entry 6xt7
Summary information and primary citation
- PDB-id
- 6xt7
- Class
- DNA
- Method
- X-ray (1.56 Å)
- Summary
- Tel25 hybrid four-quartet g-quadruplex with k+
- Reference
- Beseiso D, Chen EV, McCarthy SE, Martin KN, Gallagher EP, Miao J, Yatsunyk LA (2022): "The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes." Nucleic Acids Res., 50, 2959-2972. doi: 10.1093/nar/gkac091.
- Abstract
- G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3'-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5'-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.
- G4 notes
- 16 G-tetrads, 4 G4 helices, 4 G4 stems, UUDU, hybrid1, 3+1, 3(-P-Lw-Ln)
Cartoon-block schematics in six views (download the tarball)
List of 16 G-tetrads
1 glyco-bond=s-ss sugar=3--- groove=wn-- planarity=0.202 type=other N+ nts=4 GGGG A.DG1001,A.DG1019,A.DG1022,A.DG1004 2 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.173 type=other O+ nts=4 GGGG A.DG1005,A.DG1010,A.DG1018,A.DG1023 3 glyco-bond=--s- sugar=---. groove=-wn- planarity=0.181 type=other O+ nts=4 GGGG A.DG1006,A.DG1011,A.DG1017,A.DG1024 4 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.346 type=bowl O+ nts=4 GGGG A.DG1007,A.DG1012,A.DG1016,A.DG1025 5 glyco-bond=s-ss sugar=3--- groove=wn-- planarity=0.218 type=other N+ nts=4 GGGG B.DG1001,B.DG1019,B.DG1022,B.DG1004 6 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.177 type=other O+ nts=4 GGGG B.DG1005,B.DG1010,B.DG1018,B.DG1023 7 glyco-bond=--s- sugar=---3 groove=-wn- planarity=0.177 type=other O+ nts=4 GGGG B.DG1006,B.DG1011,B.DG1017,B.DG1024 8 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.335 type=bowl O+ nts=4 GGGG B.DG1007,B.DG1012,B.DG1016,B.DG1025 9 glyco-bond=s-ss sugar=3.-- groove=wn-- planarity=0.208 type=other N+ nts=4 GGGG C.DG1001,C.DG1019,C.DG1022,C.DG1004 10 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.191 type=other O+ nts=4 GGGG C.DG1005,C.DG1010,C.DG1018,C.DG1023 11 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.175 type=other O+ nts=4 GGGG C.DG1006,C.DG1011,C.DG1017,C.DG1024 12 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.375 type=bowl O+ nts=4 GGGG C.DG1007,C.DG1012,C.DG1016,C.DG1025 13 glyco-bond=s-ss sugar=3.-- groove=wn-- planarity=0.205 type=other N+ nts=4 GGGG D.DG1001,D.DG1019,D.DG1022,D.DG1004 14 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.161 type=other O+ nts=4 GGGG D.DG1005,D.DG1010,D.DG1018,D.DG1023 15 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.161 type=other O+ nts=4 GGGG D.DG1006,D.DG1011,D.DG1017,D.DG1024 16 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.340 type=bowl O+ nts=4 GGGG D.DG1007,D.DG1012,D.DG1016,D.DG1025
List of 4 G4-helices
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-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=s-ss sugar=3--- groove=wn-- Major-->WC N+ nts=4 GGGG A.DG1001,A.DG1019,A.DG1022,A.DG1004 2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG1010,A.DG1018,A.DG1023,A.DG1005 3 glyco-bond=-s-- sugar=--.- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG1011,A.DG1017,A.DG1024,A.DG1006 4 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG1012,A.DG1016,A.DG1025,A.DG1007 step#1 mm(<>,outward) area=15.48 rise=3.48 twist=15.5 step#2 pm(>>,forward) area=9.49 rise=3.43 twist=31.9 step#3 pm(>>,forward) area=14.01 rise=3.47 twist=24.4 strand#1 DNA glyco-bond=s--- sugar=3--- nts=4 GGGG A.DG1001,A.DG1010,A.DG1011,A.DG1012 strand#2 DNA glyco-bond=-sss sugar=---- nts=4 GGGG A.DG1019,A.DG1018,A.DG1017,A.DG1016 strand#3 DNA glyco-bond=s--- sugar=--.- nts=4 GGGG A.DG1022,A.DG1023,A.DG1024,A.DG1025 strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG A.DG1004,A.DG1005,A.DG1006,A.DG1007 |
| 3 stacking diagrams | |
|
1 glyco-bond=s-ss sugar=3--- groove=wn-- Major-->WC N+ nts=4 GGGG A.DG1001,A.DG1019,A.DG1022,A.DG1004 |
|
2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG1010,A.DG1018,A.DG1023,A.DG1005 |
|
3 glyco-bond=-s-- sugar=--.- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG1011,A.DG1017,A.DG1024,A.DG1006 |
Helix#2, 4 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=s-ss sugar=3--- groove=wn-- Major-->WC N+ nts=4 GGGG B.DG1001,B.DG1019,B.DG1022,B.DG1004 2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG B.DG1010,B.DG1018,B.DG1023,B.DG1005 3 glyco-bond=-s-- sugar=--3- groove=wn-- WC-->Major O+ nts=4 GGGG B.DG1011,B.DG1017,B.DG1024,B.DG1006 4 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG B.DG1012,B.DG1016,B.DG1025,B.DG1007 step#1 mm(<>,outward) area=15.76 rise=3.50 twist=15.4 step#2 pm(>>,forward) area=9.02 rise=3.40 twist=32.0 step#3 pm(>>,forward) area=13.62 rise=3.50 twist=24.9 strand#1 DNA glyco-bond=s--- sugar=3--- nts=4 GGGG B.DG1001,B.DG1010,B.DG1011,B.DG1012 strand#2 DNA glyco-bond=-sss sugar=---- nts=4 GGGG B.DG1019,B.DG1018,B.DG1017,B.DG1016 strand#3 DNA glyco-bond=s--- sugar=--3- nts=4 GGGG B.DG1022,B.DG1023,B.DG1024,B.DG1025 strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG B.DG1004,B.DG1005,B.DG1006,B.DG1007 |
| 3 stacking diagrams | |
|
1 glyco-bond=s-ss sugar=3--- groove=wn-- Major-->WC N+ nts=4 GGGG B.DG1001,B.DG1019,B.DG1022,B.DG1004 |
|
2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG B.DG1010,B.DG1018,B.DG1023,B.DG1005 |
|
3 glyco-bond=-s-- sugar=--3- groove=wn-- WC-->Major O+ nts=4 GGGG B.DG1011,B.DG1017,B.DG1024,B.DG1006 |
Helix#3, 4 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=s-ss sugar=3.-- groove=wn-- Major-->WC N+ nts=4 GGGG C.DG1001,C.DG1019,C.DG1022,C.DG1004 2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG C.DG1010,C.DG1018,C.DG1023,C.DG1005 3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG C.DG1011,C.DG1017,C.DG1024,C.DG1006 4 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG C.DG1012,C.DG1016,C.DG1025,C.DG1007 step#1 mm(<>,outward) area=15.19 rise=3.49 twist=16.3 step#2 pm(>>,forward) area=9.23 rise=3.41 twist=32.4 step#3 pm(>>,forward) area=14.61 rise=3.48 twist=24.4 strand#1 DNA glyco-bond=s--- sugar=3--- nts=4 GGGG C.DG1001,C.DG1010,C.DG1011,C.DG1012 strand#2 DNA glyco-bond=-sss sugar=.--- nts=4 GGGG C.DG1019,C.DG1018,C.DG1017,C.DG1016 strand#3 DNA glyco-bond=s--- sugar=---- nts=4 GGGG C.DG1022,C.DG1023,C.DG1024,C.DG1025 strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG C.DG1004,C.DG1005,C.DG1006,C.DG1007 |
| 3 stacking diagrams | |
|
1 glyco-bond=s-ss sugar=3.-- groove=wn-- Major-->WC N+ nts=4 GGGG C.DG1001,C.DG1019,C.DG1022,C.DG1004 |
|
2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG C.DG1010,C.DG1018,C.DG1023,C.DG1005 |
|
3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG C.DG1011,C.DG1017,C.DG1024,C.DG1006 |
Helix#4, 4 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=s-ss sugar=3.-- groove=wn-- Major-->WC N+ nts=4 GGGG D.DG1001,D.DG1019,D.DG1022,D.DG1004 2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG D.DG1010,D.DG1018,D.DG1023,D.DG1005 3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG D.DG1011,D.DG1017,D.DG1024,D.DG1006 4 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG D.DG1012,D.DG1016,D.DG1025,D.DG1007 step#1 mm(<>,outward) area=14.81 rise=3.48 twist=16.1 step#2 pm(>>,forward) area=9.23 rise=3.41 twist=31.7 step#3 pm(>>,forward) area=14.58 rise=3.47 twist=24.4 strand#1 DNA glyco-bond=s--- sugar=3--- nts=4 GGGG D.DG1001,D.DG1010,D.DG1011,D.DG1012 strand#2 DNA glyco-bond=-sss sugar=.--- nts=4 GGGG D.DG1019,D.DG1018,D.DG1017,D.DG1016 strand#3 DNA glyco-bond=s--- sugar=---- nts=4 GGGG D.DG1022,D.DG1023,D.DG1024,D.DG1025 strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG D.DG1004,D.DG1005,D.DG1006,D.DG1007 |
| 3 stacking diagrams | |
|
1 glyco-bond=s-ss sugar=3.-- groove=wn-- Major-->WC N+ nts=4 GGGG D.DG1001,D.DG1019,D.DG1022,D.DG1004 |
|
2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG D.DG1010,D.DG1018,D.DG1023,D.DG1005 |
|
3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG D.DG1011,D.DG1017,D.DG1024,D.DG1006 |
List of 4 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, 3 G-tetrads, 3 loops, INTRA-molecular, UUDU, hybrid1, 3+1, 3(-P-Lw-Ln)
|
1 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG A.DG1005,A.DG1010,A.DG1018,A.DG1023 2 glyco-bond=--s- sugar=---. groove=-wn- WC-->Major O+ nts=4 GGGG A.DG1006,A.DG1011,A.DG1017,A.DG1024 3 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG A.DG1007,A.DG1012,A.DG1016,A.DG1025 step#1 pm(>>,forward) area=9.49 rise=3.43 twist=31.9 step#2 pm(>>,forward) area=14.01 rise=3.47 twist=24.4 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG1005,A.DG1006,A.DG1007 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG1010,A.DG1011,A.DG1012 strand#3 D DNA glyco-bond=sss sugar=--- nts=3 GGG A.DG1018,A.DG1017,A.DG1016 strand#4 U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG1023,A.DG1024,A.DG1025 loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT1008,A.DT1009 loop#2 type=lateral strands=[#2,#3] nts=3 GTT A.DG1013,A.DT1014,A.DT1015 loop#3 type=lateral strands=[#3,#4] nts=4 GTTG A.DG1019,A.DT1020,A.DT1021,A.DG1022 |
Stem#2, 3 G-tetrads, 3 loops, INTRA-molecular, UUDU, hybrid1, 3+1, 3(-P-Lw-Ln)
|
1 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG B.DG1005,B.DG1010,B.DG1018,B.DG1023 2 glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major O+ nts=4 GGGG B.DG1006,B.DG1011,B.DG1017,B.DG1024 3 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG B.DG1007,B.DG1012,B.DG1016,B.DG1025 step#1 pm(>>,forward) area=9.02 rise=3.40 twist=32.0 step#2 pm(>>,forward) area=13.62 rise=3.50 twist=24.9 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG1005,B.DG1006,B.DG1007 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG1010,B.DG1011,B.DG1012 strand#3 D DNA glyco-bond=sss sugar=--- nts=3 GGG B.DG1018,B.DG1017,B.DG1016 strand#4 U DNA glyco-bond=--- sugar=-3- nts=3 GGG B.DG1023,B.DG1024,B.DG1025 loop#1 type=propeller strands=[#1,#2] nts=2 TT B.DT1008,B.DT1009 loop#2 type=lateral strands=[#2,#3] nts=3 GTT B.DG1013,B.DT1014,B.DT1015 loop#3 type=lateral strands=[#3,#4] nts=4 GTTG B.DG1019,B.DT1020,B.DT1021,B.DG1022 |
Stem#3, 3 G-tetrads, 3 loops, INTRA-molecular, UUDU, hybrid1, 3+1, 3(-P-Lw-Ln)
|
1 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG C.DG1005,C.DG1010,C.DG1018,C.DG1023 2 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG C.DG1006,C.DG1011,C.DG1017,C.DG1024 3 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG C.DG1007,C.DG1012,C.DG1016,C.DG1025 step#1 pm(>>,forward) area=9.23 rise=3.41 twist=32.4 step#2 pm(>>,forward) area=14.61 rise=3.48 twist=24.4 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG1005,C.DG1006,C.DG1007 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG1010,C.DG1011,C.DG1012 strand#3 D DNA glyco-bond=sss sugar=--- nts=3 GGG C.DG1018,C.DG1017,C.DG1016 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG1023,C.DG1024,C.DG1025 loop#1 type=propeller strands=[#1,#2] nts=2 TT C.DT1008,C.DT1009 loop#2 type=lateral strands=[#2,#3] nts=3 GTT C.DG1013,C.DT1014,C.DT1015 loop#3 type=lateral strands=[#3,#4] nts=4 GTTG C.DG1019,C.DT1020,C.DT1021,C.DG1022 |
Stem#4, 3 G-tetrads, 3 loops, INTRA-molecular, UUDU, hybrid1, 3+1, 3(-P-Lw-Ln)
|
1 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG D.DG1005,D.DG1010,D.DG1018,D.DG1023 2 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG D.DG1006,D.DG1011,D.DG1017,D.DG1024 3 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG D.DG1007,D.DG1012,D.DG1016,D.DG1025 step#1 pm(>>,forward) area=9.23 rise=3.41 twist=31.7 step#2 pm(>>,forward) area=14.58 rise=3.47 twist=24.4 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG1005,D.DG1006,D.DG1007 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG1010,D.DG1011,D.DG1012 strand#3 D DNA glyco-bond=sss sugar=--- nts=3 GGG D.DG1018,D.DG1017,D.DG1016 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG1023,D.DG1024,D.DG1025 loop#1 type=propeller strands=[#1,#2] nts=2 TT D.DT1008,D.DT1009 loop#2 type=lateral strands=[#2,#3] nts=3 GTT D.DG1013,D.DT1014,D.DT1015 loop#3 type=lateral strands=[#3,#4] nts=4 GTTG D.DG1019,D.DT1020,D.DT1021,D.DG1022 |
List of 8 non-stem G4-loops (including the two closing Gs)
1 type=lateral helix=#1 nts=4 GTTG A.DG1001,A.DT1002,A.DT1003,A.DG1004 2 type=lateral helix=#1 nts=4 GTTG A.DG1019,A.DT1020,A.DT1021,A.DG1022 3 type=lateral helix=#2 nts=4 GTTG B.DG1001,B.DT1002,B.DT1003,B.DG1004 4 type=lateral helix=#2 nts=4 GTTG B.DG1019,B.DT1020,B.DT1021,B.DG1022 5 type=lateral helix=#3 nts=4 GTTG C.DG1001,C.DT1002,C.DT1003,C.DG1004 6 type=lateral helix=#3 nts=4 GTTG C.DG1019,C.DT1020,C.DT1021,C.DG1022 7 type=lateral helix=#4 nts=4 GTTG D.DG1001,D.DT1002,D.DT1003,D.DG1004 8 type=lateral helix=#4 nts=4 GTTG D.DG1019,D.DT1020,D.DT1021,D.DG1022