7THB
Crystal structure of an RNA-5'/DNA-3' strand exchange junction
Summary for 7THB
| Entry DOI | 10.2210/pdb7thb/pdb |
| Descriptor | DNA (5'-D(*GP*TP*AP*AP*GP*CP*AP*GP*CP*AP*TP*C)-3'), RNA (5'-R(*AP*GP*CP*UP*UP*AP*C)-3'), DNA (5'-D(*GP*AP*TP*GP*CP*TP*C)-3'), ... (4 entities in total) |
| Functional Keywords | strand exchange junction, dna, rna, dna:dna duplex, rna:dna hybrid, a-form/b-form junction, nucleic acid, dna-rna hybrid |
| Biological source | Synthetic construct More |
| Total number of polymer chains | 9 |
| Total formula weight | 23898.55 |
| Authors | Cofsky, J.C.,Knott, G.J.,Gee, C.L.,Doudna, J.A. (deposition date: 2022-01-10, release date: 2022-04-27, Last modification date: 2024-04-03) |
| Primary citation | Cofsky, J.C.,Knott, G.J.,Gee, C.L.,Doudna, J.A. Crystal structure of an RNA/DNA strand exchange junction. Plos One, 17:e0263547-e0263547, 2022 Cited by PubMed Abstract: Short segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types-an RNA:DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-5'/DNA-3' strand exchange junction at an anisotropic resolution of 1.6 to 2.2 Å. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events. PubMed: 35436289DOI: 10.1371/journal.pone.0263547 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.64 Å) |
Structure validation
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