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- PDB-36pd: P. fulva VIPR Ternary Complex with four subunits -

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Basic information

Entry
Database: PDB / ID: 36pd
TitleP. fulva VIPR Ternary Complex with four subunits
Components
  • Target Strand
  • Vipr protein
  • viprRNA
KeywordsRNA BINDING PROTEIN/RNA / Ribonucleoprotein / VIPR / RNA Binding Protein / Ternary Complex / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
Pseudomonas fulva (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 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: Yoon, P.H. / Docter, T.A. / Zhang, Z.T. / Loi, K. / Lopez, S.C. / Valentin-Alvarado, L.E. / Tuck, O. / Brohawn, S.G. / Doudna, J.A.
History
DepositionJun 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Target Strand
L: viprRNA
A: Vipr protein
B: Vipr protein
C: Vipr protein
D: Vipr protein


Theoretical massNumber of molelcules
Total (without water)106,5546
Polymers106,5546
Non-polymers00
Water1086
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 Target Strand


Mass: 3665.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Unknown host genomic sequence. Modeled to match vrRNA.
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: RNA chain viprRNA


Mass: 6548.024 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)
#3: Protein
Vipr protein


Mass: 24085.209 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Pseudomonas fulva prophage / Source: (gene. exp.) Pseudomonas fulva (bacteria) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: Ternary complex of a P. fulva prophage VIPR system with an unknown substrate, showing 4 subunits.
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: unidentified (others) / Strain: Pseudomonas fulva prophage
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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210297 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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