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- EMDB-47658: Cryo-EM structure of RaiA RNA from Mogibacterium pumilum -

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Basic information

Entry
Database: EMDB / ID: EMD-47658
TitleCryo-EM structure of RaiA RNA from Mogibacterium pumilum
Map data
Sample
  • Complex: RaiA RNA from Mogibacterium pumilum
    • RNA: RNA (155-MER)
KeywordsNon-coding RNA / cryo-EM / raiA motif RNA / ModT / RNA
Biological speciesMogibacterium pumilum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHe Y / Zhong J / Yang Y / Gunsalus RP / Zhou ZH / Feigon J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131901 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
CitationJournal: To Be Published
Title: Cryo-EM structures reveal a conserved architecture for RaiA non-coding RNA
Authors: He Y / Zhong J / Yang Y / Gunsalus RP / Zhou ZH / Feigon J
History
DepositionOct 31, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47658.png

Downloads & links

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Map

FileDownload / File: emd_47658.map.gz / Format: CCP4 / Size: 64 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.)
0.86 Å/pix.
x 256 pix.
= 219.136 Å		0.86 Å/pix.
x 256 pix.
= 219.136 Å		0.86 Å/pix.
x 256 pix.
= 219.136 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.036118694 - 0.15199053
Average (Standard dev.)0.00028797679 (±0.004380014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.136 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47658_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_47658_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47658_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : RaiA RNA from Mogibacterium pumilum

EntireName: RaiA RNA from Mogibacterium pumilum
Components
  • Complex: RaiA RNA from Mogibacterium pumilum
    • RNA: RNA (155-MER)

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Supramolecule #1: RaiA RNA from Mogibacterium pumilum

SupramoleculeName: RaiA RNA from Mogibacterium pumilum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mogibacterium pumilum (bacteria)

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Macromolecule #1: RNA (155-MER)

MacromoleculeName: RNA (155-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Mogibacterium pumilum (bacteria)
Molecular weightTheoretical: 53.632918 KDa
SequenceString:
GGUAAGGUCA UGUUCGUGGU UGAAAGUCCA AGCCAGCUAC GGGCAAAGGG AUCCACGUAA GCUGCUGCGG AGACGGCAGU GAUCAUGGC GUAGCUUAGA AGUAAGUCCU CCGGGAAACU CGGGUUAAGG CAAGUGUGGG GUCAAAAACC AGGUCGAGUG G CCUUG

GENBANK: GENBANK: CP016199.1

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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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 343947
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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