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- EMDB-49229: RNA scaffold attached to 8-oxoguanine riboswitch aptamer core only -

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Basic information

Entry
Database: EMDB / ID: EMD-49229
TitleRNA scaffold attached to 8-oxoguanine riboswitch aptamer core only
Map data
Sample
  • Complex: Scaffold RNA attached to 8-oxoguanine aptamer bound to 8-oxoguanine
    • RNA: RNA (88-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordsviral RNA / scaffold / engineering / RNA
Biological speciesunidentified (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsJones CP / Ferre-D'Amare AR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: Symmetric scaffolds enable de novo modelling of RNA by cryoEM
Authors: Jones CP / Ferre-D'Amare AR
History
DepositionFeb 13, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49229.png

Downloads & links

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Map

FileDownload / File: emd_49229.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 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: 0.1
Minimum - Maximum-0.22414829 - 1.0832367
Average (Standard dev.)0.003964783 (±0.02951254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49229_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Locally sharpened map

Fileemd_49229_additional_1.map
AnnotationLocally sharpened map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_49229_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_49229_half_map_2.map
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Sample components

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Entire : Scaffold RNA attached to 8-oxoguanine aptamer bound to 8-oxoguanine

EntireName: Scaffold RNA attached to 8-oxoguanine aptamer bound to 8-oxoguanine
Components
  • Complex: Scaffold RNA attached to 8-oxoguanine aptamer bound to 8-oxoguanine
    • RNA: RNA (88-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Scaffold RNA attached to 8-oxoguanine aptamer bound to 8-oxoguanine

SupramoleculeName: Scaffold RNA attached to 8-oxoguanine aptamer bound to 8-oxoguanine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: unidentified (others)

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Macromolecule #1: RNA (88-MER)

MacromoleculeName: RNA (88-MER) / type: rna / ID: 1 / Number of copies: 4
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.445496 KDa
SequenceString:
GGGCCACUGU UUCACUGUUG CGCUACAUCU CCUGUUCGUA UAACCCCGAU AAUCGGUUCG GGGGCUCUAC UGGGGUCCGU AAAAUCCUA ACUACGAACG GGAGGCCACA CGAAAGUGUG GAGUGACCAG UGGCCCCACC CUGAAGGUAA ACUUGUAGCG C

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 18 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 411 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsRNA scaffold attached to 8-oxoguanine riboswitch aptamer

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9dig


Details: The 9DIG model was used as a starting point for modelling this RNA, which was designed based on the RNA in 9DIG.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 482149
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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