ISDA: 36PD

Deposition Date 2026-06-24

Release Date 2026-09-16

Last Version Date 2026-11-04

Entry Detail

PDB ID:

36PD

Keywords:

RNA BINDING PROTEIN/RNA

Title:

P. fulva VIPR Ternary Complex with four subunits

Biological Source:

Source Organism(s):

Pseudomonas fulva (Taxon ID: 47880)
Escherichia coli (Taxon ID: 562)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.80 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Vipr protein
Chain IDs:A, B, C, D
Chain Length:212
Number of Molecules:4
Biological Source:Pseudomonas fulva

Polymer Type:polydeoxyribonucleotide
Molecule:Target Strand
Chain IDs:E (auth: K)
Chain Length:12
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:viprRNA
Chain IDs:F (auth: L)
Chain Length:20
Number of Molecules:1
Biological Source:Pseudomonas fulva

Primary Citation

VIPR RNA-guided DNA recognition by noncontiguous geometric triplex formation.

Yoon, P.H, Docter, T.A, Zhang, Z.T, Loi, K, Lopez, S.C, Valentin-Alvarado, L.E, Tuck, O.T, Brohawn, S.G, Doudna, J.A.Show

Science 393 1236 1240 (2026)

PMID: 42752121 DOI: 10.1126/science.aei3472

Abstact

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.

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Primary Citation of related structures

Abstact

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