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- EMDB-49200: RNA scaffold attached to Mango in the presence of TO1-biotin -

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Basic information

Entry
Database: EMDB / ID: EMD-49200
TitleRNA scaffold attached to Mango in the presence of TO1-biotin
Map data
Sample
  • Complex: Scaffold RNA attached to Mango in the absence of ligand
    • RNA: RNA (82-MER)
  • Ligand: 4-[(3-{2-[(2-methoxyethyl)amino]-2-oxoethyl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium
Keywordsviral RNA / scaffold / engineering / RNA
Biological speciesunidentified (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 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 12, 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_49200.png

Downloads & links

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Map

FileDownload / File: emd_49200.map.gz / Format: CCP4 / Size: 347.6 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 450 pix.
= 373.5 Å		0.83 Å/pix.
x 450 pix.
= 373.5 Å		0.83 Å/pix.
x 450 pix.
= 373.5 Å

Surface

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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-1.4982034 - 2.4756465
Average (Standard dev.)-0.000105569205 (±0.007797632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 373.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49200_msk_1.map
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AxesZYX

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Additional map: Locally sharpened map

Fileemd_49200_additional_1.map
AnnotationLocally sharpened map
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AxesZYX

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Half map: #2

Fileemd_49200_half_map_1.map
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Half map: #1

Fileemd_49200_half_map_2.map
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Sample components

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Entire : Scaffold RNA attached to Mango in the absence of ligand

EntireName: Scaffold RNA attached to Mango in the absence of ligand
Components
  • Complex: Scaffold RNA attached to Mango in the absence of ligand
    • RNA: RNA (82-MER)
  • Ligand: 4-[(3-{2-[(2-methoxyethyl)amino]-2-oxoethyl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium

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Supramolecule #1: Scaffold RNA attached to Mango in the absence of ligand

SupramoleculeName: Scaffold RNA attached to Mango in the absence of ligand
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: unidentified (others)

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Macromolecule #1: RNA (82-MER)

MacromoleculeName: RNA (82-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 41.611629 KDa
SequenceString:
GGGCCACUGU UUCACUGUUG CGCUACAUCU CCCUACGAAG GAAGGUUUGG UAUGUGGUAU AUUCGAUGGG AGGCCACACG AAAGUGUGG AGUGACCAGU GGCCCCACCC UGAAGGUAAA CUUGUAGCGC

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Macromolecule #2: 4-[(3-{2-[(2-methoxyethyl)amino]-2-oxoethyl}-1,3-benzothiazol-3-i...

MacromoleculeName: 4-[(3-{2-[(2-methoxyethyl)amino]-2-oxoethyl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium
type: ligand / ID: 2 / Number of copies: 1 / Formula: EKJ
Molecular weightTheoretical: 407.529 Da
Chemical component information

ChemComp-EKJ:
4-[(3-{2-[(2-methoxyethyl)amino]-2-oxoethyl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium

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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 Mango in the presence of TO1-biotin

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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: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 494697
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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