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- PDB-36pg: VIPR Ternary Complex with a duplex dsDNA substrate, 11 subunits -

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Basic information

Entry
Database: PDB / ID: 36pg
TitleVIPR Ternary Complex with a duplex dsDNA substrate, 11 subunits
Components
  • Non-target strand
  • SUSP1 Vipr protein
  • SUSP1 viprRNA
  • Target Strand
KeywordsRNA BINDING PROTEIN/RNA/DNA / Ribonucleoprotein / VIPR / RNA Binding Protein / Ternary Complex / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology: / DNA / DNA (> 10) / RNA / RNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesSuspvirus SUSP1
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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: 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
A: SUSP1 viprRNA
B: Target Strand
C: Non-target strand
D: SUSP1 Vipr protein
E: SUSP1 Vipr protein
F: SUSP1 Vipr protein
G: SUSP1 Vipr protein
H: SUSP1 Vipr protein
I: SUSP1 Vipr protein
J: SUSP1 Vipr protein
K: SUSP1 Vipr protein
L: SUSP1 Vipr protein
M: SUSP1 Vipr protein
N: SUSP1 Vipr protein


Theoretical massNumber of molelcules
Total (without water)322,24114
Polymers322,24114
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 SUSP1 viprRNA


Mass: 30630.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Resolvable segment of the SUSP1 viprRNA / Source: (gene. exp.) Suspvirus SUSP1 / Production host: Escherichia coli (E. coli) / References: GenBank: 1368578885
#2: DNA chain Target Strand


Mass: 19631.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: resolvable segment of the target DNA strand. / Source: (synth.) synthetic construct (others)
#3: DNA chain Non-target strand


Mass: 19204.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Resolvable segment of the non-target DNA strand / Source: (synth.) synthetic construct (others)
#4: Protein
SUSP1 Vipr protein


Mass: 22979.531 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suspvirus SUSP1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N9RUZ5
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 the SUSP1 VIPR system with a duplex dsDNA substrate with 11 subunits.
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Suspvirus SUSP1
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49155 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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