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- EMDB-49309: Scaffold attached to Mango without ligand, local refinement of co... -

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Basic information

Entry
Database: EMDB / ID: EMD-49309
TitleScaffold attached to Mango without ligand, local refinement of core, tilted data collection of tetramer
Map data
Sample
  • Complex: Scaffold attached to Mango in the absence of ligand
    • RNA: Scaffold attached to Mango in the absence of ligand
Keywordsriboswitch / RNA / engineering / aptamer
Biological speciesother sequences (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 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 19, 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_49309.png

Downloads & links

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Map

FileDownload / File: emd_49309.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.046925604 - 0.3698397
Average (Standard dev.)-0.00039630596 (±0.013531282)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49309_msk_1.map
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Additional map: #1

Fileemd_49309_additional_1.map
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Half map: #1

Fileemd_49309_half_map_1.map
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Half map: #2

Fileemd_49309_half_map_2.map
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Sample components

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Entire : Scaffold attached to Mango in the absence of ligand

EntireName: Scaffold attached to Mango in the absence of ligand
Components
  • Complex: Scaffold attached to Mango in the absence of ligand
    • RNA: Scaffold attached to Mango in the absence of ligand

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

SupramoleculeName: Scaffold attached to Mango in the absence of ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: other sequences (unknown)

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

MacromoleculeName: Scaffold attached to Mango in the absence of ligand / type: rna / ID: 1 / Details: Forms homotetramers and homodimers on the grid
Source (natural)Organism: other sequences (unknown)
SequenceString:
GGGCCACUGU UUCACUGUUG CGCUACAUCU CCCUACGAAG GAAGGUUUGG UAUGUGGUAU AUUCGAUGGG AGGCCACACG AAAGUGUGGA GUGACCAGUG GCCCCACCCU GAAGGUAAAC UUGUAGCGC

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.15 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96879
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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