DSSR-enabled G4 identification/annotation: PDB entry 1jrn
Summary information and primary citation
- PDB-id
- 1jrn
- Class
- DNA
- Method
- X-ray (2.0 Å)
- Summary
- Orthorhombic form of oxytricha telomeric DNA at 2.0a
- Reference
- Haider S, Parkinson GN, Neidle S (2002): "Crystal structure of the potassium form of an Oxytricha nova G-quadruplex." J.Mol.Biol., 320, 189-200. doi: 10.1016/S0022-2836(02)00428-X.
- Abstract
- The crystal structures of the potassium-containing quadruplex formed from the Oxytricha nova sequence d(GGGGTTTTGGGG) are reported, in two space groups, the orthorhombic P2(1)2(1)2(1) and the trigonal P3(2)21, which diffract to 2.0 A and 1.49 A, respectively. The orthorhombic form contains two independent quadruplexes in the asymmetric unit, and the trigonal form contains one. All three of these quadruplexes adopt an identical fold, with two strands forming an antiparallel diagonal arrangement. This is identical with that observed previously in NMR studies of the native sodium and potassium forms, and a crystallographic analysis of it complexed with an O. nova protein. The present analysis demonstrates that the native structure is the same in solution and in the crystalline state and, moreover, that the nature of the counter-ion does not affect the overall fold of this quadruplex. The analysis corrects an earlier crystallographic study of this quadruplex. The conformation of the tetra-thymine loop is described in detail, which involves the third thymine base folding back to interact with the first thymine base. The water networks in the grooves and loops are described and, in particular, the ability of water molecules to form a continuous spine of hydration in the narrow groove is detailed. Each quadruplex has five potassium ions organised in a linear channel, with square antiprismatic coordination to each ion from oxygen atoms.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.262 type=other -- nts=4 GGGG 1:A.DG1001,1:B.DG2004,1:A.DG1012,1:B.DG2009 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.187 type=other -- nts=4 GGGG 1:A.DG1002,1:B.DG2003,1:A.DG1011,1:B.DG2010 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.189 type=other -- nts=4 GGGG 1:A.DG1003,1:B.DG2002,1:A.DG1010,1:B.DG2011 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.274 type=bowl -- nts=4 GGGG 1:A.DG1004,1:B.DG2001,1:A.DG1009,1:B.DG2012
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, 4 G-tetrads, inter-molecular, with 1 stem
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1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1001,1:B.DG2004,1:A.DG1012,1:B.DG2009 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG1002,1:B.DG2003,1:A.DG1011,1:B.DG2010 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1003,1:B.DG2002,1:A.DG1010,1:B.DG2011 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG1004,1:B.DG2001,1:A.DG1009,1:B.DG2012 step#1 mm(<>,outward) area=13.92 rise=3.51 twist=17.9 step#2 pp(><,inward) area=17.53 rise=3.51 twist=37.6 step#3 mm(<>,outward) area=14.32 rise=3.42 twist=17.2 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG1001,1:A.DG1002,1:A.DG1003,1:A.DG1004 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:B.DG2004,1:B.DG2003,1:B.DG2002,1:B.DG2001 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG1012,1:A.DG1011,1:A.DG1010,1:A.DG1009 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:B.DG2009,1:B.DG2010,1:B.DG2011,1:B.DG2012 |
| 3 stacking diagrams | |
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1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1001,1:B.DG2004,1:A.DG1012,1:B.DG2009 |
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2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG1002,1:B.DG2003,1:A.DG1011,1:B.DG2010 |
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3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1003,1:B.DG2002,1:A.DG1010,1:B.DG2011 |
List of 1 G4-stem
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, 2 loops, inter-molecular, UDDU, anti-parallel:basket, 2+2
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1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1001,1:B.DG2004,1:A.DG1012,1:B.DG2009 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG1002,1:B.DG2003,1:A.DG1011,1:B.DG2010 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1003,1:B.DG2002,1:A.DG1010,1:B.DG2011 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG1004,1:B.DG2001,1:A.DG1009,1:B.DG2012 step#1 mm(<>,outward) area=13.92 rise=3.51 twist=17.9 step#2 pp(><,inward) area=17.53 rise=3.51 twist=37.6 step#3 mm(<>,outward) area=14.32 rise=3.42 twist=17.2 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG1001,1:A.DG1002,1:A.DG1003,1:A.DG1004 strand#2 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:B.DG2004,1:B.DG2003,1:B.DG2002,1:B.DG2001 strand#3 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG1012,1:A.DG1011,1:A.DG1010,1:A.DG1009 strand#4 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:B.DG2009,1:B.DG2010,1:B.DG2011,1:B.DG2012 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT 1:A.DT1005,1:A.DT1006,1:A.DT1007,1:A.DT1008 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT 1:B.DT2005,1:B.DT2006,1:B.DT2007,1:B.DT2008 |