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- PDB-36pr: P. fulva VIPR Ternary Complex Consensus Conformation -

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Basic information

Entry
Database: PDB / ID: 36pr
TitleP. fulva VIPR Ternary Complex Consensus Conformation
Components
  • Non-target DNA
  • P. fulva prophage protein
  • Target DNA
  • viprRNA
KeywordsRNA BINDING PROTEIN/RNA/DNA / Ribonucleoprotein / VIPR / RNA Binding Protein / Ternary Complex / RNA BINDING PROTEIN-RNA-DNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesPseudomonas fulva (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsDocter, T.A. / Yoon, P.H. / Zhang, Z. / Brohawn, S.G. / Doudna, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF 2334028 United States
CitationJournal: Science / Year: 2026
Title: VIPR RNA-guided DNA recognition by noncontiguous geometric triplex formation.
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 /
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.
History
DepositionJun 25, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update
Revision 1.1Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: viprRNA
B: Target DNA
C: Non-target DNA
D: P. fulva prophage protein
E: P. fulva prophage protein
F: P. fulva prophage protein
G: P. fulva prophage protein
H: P. fulva prophage protein
I: P. fulva prophage protein
J: P. fulva prophage protein
K: P. fulva prophage protein
L: P. fulva prophage protein
M: P. fulva prophage protein


Theoretical massNumber of molelcules
Total (without water)272,42813
Polymers272,42813
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain viprRNA


Mass: 17098.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Pseudomonas fulva prophage / Source: (gene. exp.) Pseudomonas fulva (bacteria) / Production host: Escherichia coli (E. coli)
#2: DNA chain Target DNA


Mass: 9280.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Segment of an unknown target DNA sequence. DNA segments were modeled with the following logic: vrRNA NN domains were modeled as adenosines or cytosines, the target strand was modeled as ...Details: Segment of an unknown target DNA sequence. DNA segments were modeled with the following logic: vrRNA NN domains were modeled as adenosines or cytosines, the target strand was modeled as complementary to the vrRNA with x3 bases being treated as cytosines or guanines as density permitted. The non-target strand was modeled largely as thymines, with intermittent guanines and cytosines as density permitted.
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: DNA chain Non-target DNA


Mass: 5196.351 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Segment of an unknown non-target DNA sequence. DNA segments were modeled with the following logic: vrRNA NN domains were modeled as adenosines or cytosines, the target strand was modeled as ...Details: Segment of an unknown non-target DNA sequence. DNA segments were modeled with the following logic: vrRNA NN domains were modeled as adenosines or cytosines, the target strand was modeled as complementary to the vrRNA with x3 bases being treated as cytosines or guanines as density permitted. The non-target strand was modeled largely as thymines, with intermittent guanines and cytosines as density permitted.
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#4: Protein
P. fulva prophage protein


Mass: 24085.209 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: Pseudomonas fulva prophage / Source: (gene. exp.) Pseudomonas fulva (bacteria) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Consensus Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 10 subunits.
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas fulva (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95999 / Symmetry type: POINT
RefinementHighest resolution: 2.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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