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- PDB-35se: VIPR Binary Complex - Consensus Conformation -

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Basic information

Entry
Database: PDB / ID: 35se
TitleVIPR Binary Complex - Consensus Conformation
Components
  • SUSP1 Vipr
  • SUSP1 viprRNA
KeywordsRNA BINDING PROTEIN/RNA / Ribonucleoprotein / VIPR / RNA Binding Protein / Binary Complex / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSuspvirus SUSP1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 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
DepositionMay 14, 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
G: SUSP1 Vipr
K: SUSP1 Vipr
J: SUSP1 Vipr
I: SUSP1 Vipr
H: SUSP1 Vipr
A: SUSP1 viprRNA


Theoretical massNumber of molelcules
Total (without water)124,3446
Polymers124,3446
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: Protein
SUSP1 Vipr


Mass: 22979.531 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suspvirus SUSP1 / Production host: Escherichia coli (E. coli)
#2: RNA chain SUSP1 viprRNA


Mass: 9446.579 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Resolvable fragment of a SUSP1 viprRNA. / Source: (gene. exp.) Suspvirus SUSP1 / 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: Binary complex of the SUSP1 Vipr protein with an associated viprRNA.
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
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
Specimen supportGrid type: UltrAuFoil R1.2/1.3
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: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (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: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 337932 / Symmetry type: POINT
RefinementCross valid method: NONE

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