Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	VIPR RNA-guided DNA recognition by noncontiguous geometric triplex formation.
Journal, issue, pages	Science, Vol. 393, Issue 6817, Page 1236-1240, Year 2026
Publish date	Sep 17, 2026
Authors	Peter H Yoon / Trevor A Docter / Zeyuan Terry Zhang / Kenneth Loi / Santiago C Lopez / Luis E Valentin-Alvarado / Owen T Tuck / Stephen G Brohawn / Jennifer A Doudna /
PubMed Abstract	Viral interference programmable repeat (VIPR) systems use a noncontiguous code for RNA-guided transcriptional silencing. How the Vipr protein and a VIPR RNA (vrRNA) comprising alternating GGY and NN ...Viral interference programmable repeat (VIPR) systems use a noncontiguous code for RNA-guided transcriptional silencing. How the Vipr protein and a VIPR RNA (vrRNA) comprising alternating GGY and NN segments achieve precise DNA targeting is unknown. Here, we present 21 cryo-electron microscopy structures that help explain the mechanism of target engagement. Vipr protomers oligomerize along the vrRNA to form a right-handed helical filament, sequestering each GGY motif and positioning the adjacent NN bases for target base pairing. DNA binding, in which every third nucleotide is skipped, results in a gapped vrRNA-DNA hybrid helix that encircles the nontarget DNA strand to form a geometric triplex. These findings suggest that triplex-mediated target-strand handoff could enable noncontiguous and programmable RNA-guided DNA recognition in VIPR systems.
External links	Science / PubMed:42752121
Methods	EM (single particle)
Resolution	2.5 - 3.5 Å
Structure data	77155 35se EMDB-77155, PDB-35se: VIPR Binary Complex - Consensus Conformation Method: EM (single particle) / Resolution: 2.68 Å 77156 35sf EMDB-77156, PDB-35sf: VIPR Binary Complex with one filament Method: EM (single particle) / Resolution: 2.85 Å 77157 35sg EMDB-77157, PDB-35sg: VIPR Binary Complex with two filaments Method: EM (single particle) / Resolution: 2.7 Å 77176 35sy EMDB-77176, PDB-35sy: VIPR Ternary Complex with a pre-unwound dsDNA substrate, 11 subunits Method: EM (single particle) / Resolution: 3.17 Å 77183 35tr EMDB-77183, PDB-35tr: VIPR Ternary Complex with a pre-unwound dsDNA substrate, 12 subunits Method: EM (single particle) / Resolution: 3.13 Å 77184 35tw EMDB-77184, PDB-35tw: VIPR Ternary Complex with an ssRNA substrate, Closed Conformation Method: EM (single particle) / Resolution: 2.94 Å 77185 35tx EMDB-77185, PDB-35tx: VIPR Ternary Complex with an ssRNA substrate, Closed Conformation, 11 subunits Method: EM (single particle) / Resolution: 2.76 Å 77731 36pb EMDB-77731, PDB-36pb: VIPR Ternary Complex with an ssDNA substrate, 10 subunits Method: EM (single particle) / Resolution: 3.1 Å 77732 36pc EMDB-77732, PDB-36pc: VIPR Ternary Complex with an ssDNA substrate, 11 subunits Method: EM (single particle) / Resolution: 3.0 Å 77733 36pd EMDB-77733, PDB-36pd: P. fulva VIPR Ternary Complex with four subunits Method: EM (single particle) / Resolution: 2.8 Å 77734 36pe EMDB-77734, PDB-36pe: VIPR Ternary Complex with an ssDNA substrate, 12 subunits Method: EM (single particle) / Resolution: 3.0 Å 77735 36pf EMDB-77735, PDB-36pf: VIPR Ternary Complex with a duplex dsDNA substrate, 5 subunits Method: EM (single particle) / Resolution: 3.4 Å 77736 36pg EMDB-77736, PDB-36pg: VIPR Ternary Complex with a duplex dsDNA substrate, 11 subunits Method: EM (single particle) / Resolution: 3.5 Å 77738 36pj EMDB-77738, PDB-36pj: VIPR Ternary Complex with a duplex dsDNA substrate, 7 subunits Method: EM (single particle) / Resolution: 3.2 Å 77739 36pk EMDB-77739, PDB-36pk: VIPR Ternary Complex with a duplex dsDNA substrate, 10 subunits Method: EM (single particle) / Resolution: 3.3 Å 77740 36pm EMDB-77740, PDB-36pm: VIPR Ternary Complex with a duplex dsDNA substrate, 9 subunits Method: EM (single particle) / Resolution: 3.2 Å 77742 36po EMDB-77742, PDB-36po: VIPR Ternary Complex with a duplex dsDNA substrate, 8 subunits Method: EM (single particle) / Resolution: 3.2 Å 77745 36pr EMDB-77745, PDB-36pr: P. fulva VIPR Ternary Complex Consensus Conformation Method: EM (single particle) / Resolution: 2.5 Å
Chemicals	ChemComp-HOH: WATER
Source	suspvirus susp1 synthetic construct (others) unidentified (others) escherichia coli (E. coli) pseudomonas fulva (bacteria)
Keywords	RNA BINDING PROTEIN/RNA / Ribonucleoprotein / VIPR / RNA Binding Protein / Binary Complex / RNA BINDING PROTEIN-RNA complex / RNA BINDING PROTEIN/RNA/DNA / Ternary Complex / RNA BINDING PROTEIN-RNA-DNA complex