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- EMDB-73141: De Novo RNA Pseudocycle, pC2-240-0 -

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Basic information

Entry
Database: EMDB / ID: EMD-73141
TitleDe Novo RNA Pseudocycle, pC2-240-0
Map dataMain Map, Non Uniform Refinement, Half Map B
Sample
  • Complex: De Novo RNA Pseudocycle, pC2-240-0
    • RNA: pC2-240-04: RNA (240-MER)
KeywordsDe Novo RNA / RNA Pseudocycle / pC2-240-0 / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.63 Å
AuthorsWeidle C / Favor A
Funding support United States, 4 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-043758 United States
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)CHE-2226466 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)NIGMS GM148166 United States
CitationJournal: To Be Published
Title: De novo design of RNA and nucleoprotein complexes
Authors: Favor A / Quijano R / Chernova E / Kubaney A / Weidle C / Esler MA / McHugh L / Carr A / Hsia Y / Juergens D / Carr KD / Kim PT / Politanska Y / Sehgal E / Kwon PS / Pecoraro RJ / Glasscock ...Authors: Favor A / Quijano R / Chernova E / Kubaney A / Weidle C / Esler MA / McHugh L / Carr A / Hsia Y / Juergens D / Carr KD / Kim PT / Politanska Y / Sehgal E / Kwon PS / Pecoraro RJ / Glasscock C / Borst AJ / DiMaio F / Stoddard BL / Baker D
History
DepositionOct 10, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73141.png

Downloads & links

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Map

FileDownload / File: emd_73141.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Map, Non Uniform Refinement, Half Map B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0658
Minimum - Maximum-0.09504307 - 0.28659213
Average (Standard dev.)-0.000018897068 (±0.0071784463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Main Map, Non Uniform Refinement, Unsharpened

Fileemd_73141_half_map_1.map
AnnotationMain Map, Non Uniform Refinement, Unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Main Map, Non Uniform Refinement, Half Map A

Fileemd_73141_half_map_2.map
AnnotationMain Map, Non Uniform Refinement, Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : De Novo RNA Pseudocycle, pC2-240-0

EntireName: De Novo RNA Pseudocycle, pC2-240-0
Components
  • Complex: De Novo RNA Pseudocycle, pC2-240-0
    • RNA: pC2-240-04: RNA (240-MER)

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Supramolecule #1: De Novo RNA Pseudocycle, pC2-240-0

SupramoleculeName: De Novo RNA Pseudocycle, pC2-240-0 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 77.16 KDa

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Macromolecule #1: pC2-240-04: RNA (240-MER)

MacromoleculeName: pC2-240-04: RNA (240-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 78.390711 KDa
SequenceString: GGAAAGCUCC CGUCCCAGCC CGACGGGGGU AUAAGGGCGC CCGUAGGCGC ACCUCGAUGA CCAGUCGAGG UUGCGCCAGC CGGGGGGCG AUGGCCCCUG ACCACACGCA GGGACAAUGC CCCAAAGGAC AUGUCCCAGC CCCCGUCGGG UAUAAGGGCG C CCGUAGGC ...String:
GGAAAGCUCC CGUCCCAGCC CGACGGGGGU AUAAGGGCGC CCGUAGGCGC ACCUCGAUGA CCAGUCGAGG UUGCGCCAGC CGGGGGGCG AUGGCCCCUG ACCACACGCA GGGACAAUGC CCCAAAGGAC AUGUCCCAGC CCCCGUCGGG UAUAAGGGCG C CCGUAGGC GCACCUCCAU GACCAGUGGA GGUAGCGCCA GUCAGGGGCC GAUGCCCCCC GGCCAUACGU AGGGACGAGG GC GA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration43 mg/mL
BufferpH: 8 / Component - Concentration: 10.0 mM / Component - Formula: MgCl2 / Component - Name: Magnesium Chloride / Details: 10 mM Magnesium Chloride,
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa / Details: 15
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Details10 mM MgCl2

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 5 / Number real images: 8030 / Average exposure time: 5.0 sec. / Average electron dose: 48.739 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5482343 / Details: particles from template picking
CTF correctionSoftware - Name: cryoSPARC / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab Initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: Non Uniform Refinement / Number images used: 140174
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Avg.num./class: 57048 / Software - Name: cryoSPARC / Details: Heterogeneous Refinement
FSC plot (resolution estimation)

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