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- PDB-9h86: Small circular RNA dimer - Class 4 -

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Basic information

Entry
Database: PDB / ID: 9h86
TitleSmall circular RNA dimer - Class 4
Components
  • Circular RNA
  • Complementary strand
KeywordsRNA / small RNA circles / dimer / RNA crossover
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsMcRae, E.K. / Kristoffersen, E.L. / Holliger, P. / Andersen, E.S.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0070452 Denmark
CitationJournal: To Be Published
Title: Roles of dimeric intermediates in RNA-catalyzed rolling circle synthesis
Authors: Kristoffersen, E.L. / McRae, E.K. / Sorensen, N.R. / Holliger, P. / Andersen, E.S.
History
DepositionOct 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complementary strand
D: Circular RNA
C: Circular RNA
B: Complementary strand
E: Complementary strand
H: Circular RNA
G: Circular RNA
F: Complementary strand


Theoretical massNumber of molelcules
Total (without water)92,0358
Polymers92,0358
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
Complementary strand


Mass: 11817.235 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: RNA chain
Circular RNA


Mass: 11191.466 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Circular RNA / Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
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: Dimer intermediate class 2 composed of 2 circular RNA and 2 complimentary RNA
Type: COMPLEX / Details: Dimer prepared by annealing / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K

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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 magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6820
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.3particle selection
2EPUimage acquisition
4cryoSPARC4.5.3CTF correction
7UCSF ChimeraX1.6.1model fitting
11cryoSPARC4.5.3classification
12cryoSPARC4.5.33D reconstructionNU-refinement
13PHENIX1.21.2-5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 668921
3D reconstructionResolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26859 / Symmetry type: POINT
Atomic model buildingB value: 231 / Protocol: OTHER / Space: REAL
RefinementCross valid method: NONE

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