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- EMDB-62991: Clostridium botulinum ncRNA homo-dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-62991
TitleClostridium botulinum ncRNA homo-dimer
Map data
Sample
  • Complex: Clostridium botulinum OLE RNA dimer
    • RNA: RNA (578-MER)
  • Ligand: MAGNESIUM ION
KeywordsncRNA / CryoEM / RNA
Biological speciesClostridium botulinum A str. ATCC 19397 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJia XY / Wang L / Su ZM
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222040 China
CitationJournal: Science / Year: 2025
Title: Cryo-EM reveals mechanisms of natural RNA multivalency.
Authors: Liu Wang / Jiahao Xie / Tao Gong / Hao Wu / Yifan Tu / Xin Peng / Sitong Shang / Xinyu Jia / Haiyun Ma / Jian Zou / Sheng Xu / Xin Zheng / Dong Zhang / Yang Liu / Chong Zhang / Yongbo Luo / ...Authors: Liu Wang / Jiahao Xie / Tao Gong / Hao Wu / Yifan Tu / Xin Peng / Sitong Shang / Xinyu Jia / Haiyun Ma / Jian Zou / Sheng Xu / Xin Zheng / Dong Zhang / Yang Liu / Chong Zhang / Yongbo Luo / Zirui Huang / Bin Shao / Binwu Ying / Yu Cheng / Yingqiang Guo / Ying Lai / Dingming Huang / Jianquan Liu / Yuquan Wei / Siqi Sun / Xuedong Zhou / Zhaoming Su /
Abstract: Homo-oligomerization of biological macromolecules leads to functional assemblies that are critical to understanding various cellular processes. However, RNA quaternary structures have rarely been ...Homo-oligomerization of biological macromolecules leads to functional assemblies that are critical to understanding various cellular processes. However, RNA quaternary structures have rarely been reported. Comparative genomics analysis has identified RNA families containing hundreds of sequences that adopt conserved secondary structures and likely fold into complex three-dimensional structures. In this study, we used cryo-electron microscopy (cryo-EM) to determine structures from four RNA families, including ARRPOF and OLE forming dimers and ROOL and GOLLD forming hexameric, octameric, and dodecameric nanostructures, at 2.6- to 4.6-angstrom resolutions. These homo-oligomeric assemblies reveal a plethora of structural motifs that contribute to RNA multivalency, including kissing-loop, palindromic base-pairing, A-stacking, metal ion coordination, pseudoknot, and minor-groove interactions. These results provide the molecular basis of intermolecular interactions driving RNA multivalency with potential functional relevance.
History
DepositionJan 5, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62991.png

Downloads & links

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Map

FileDownload / File: emd_62991.map.gz / Format: CCP4 / Size: 274.6 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.)
0.85 Å/pix.
x 416 pix.
= 353.6 Å		0.85 Å/pix.
x 416 pix.
= 353.6 Å		0.85 Å/pix.
x 416 pix.
= 353.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.92218834 - 1.3570279
Average (Standard dev.)0.00051207433 (±0.014122744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 353.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62991_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_62991_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Clostridium botulinum OLE RNA dimer

EntireName: Clostridium botulinum OLE RNA dimer
Components
  • Complex: Clostridium botulinum OLE RNA dimer
    • RNA: RNA (578-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Clostridium botulinum OLE RNA dimer

SupramoleculeName: Clostridium botulinum OLE RNA dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Clostridium botulinum A str. ATCC 19397 (bacteria)

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Macromolecule #1: RNA (578-MER)

MacromoleculeName: RNA (578-MER) / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: Clostridium botulinum A str. ATCC 19397 (bacteria)
Molecular weightTheoretical: 186.772516 KDa
SequenceString: GGUGCAGUAU UCUAGUCAGG UAAGUAUAUC UUGAAGGCGG GGCUAAAAAU CCGCUAAAGG GCACAUCGAU GAAGCUUCUG GUGCUGGCU UACGACGCCC AGUUGUGGGC UGGUGCUGGG AGAAAGAAGG CUGGGGCAAU CACAAAGGCA UGUGGCAACU G ACCCUACC ...String:
GGUGCAGUAU UCUAGUCAGG UAAGUAUAUC UUGAAGGCGG GGCUAAAAAU CCGCUAAAGG GCACAUCGAU GAAGCUUCUG GUGCUGGCU UACGACGCCC AGUUGUGGGC UGGUGCUGGG AGAAAGAAGG CUGGGGCAAU CACAAAGGCA UGUGGCAACU G ACCCUACC UUCGUGGAGG CCAUUGAUUG UGUAUAGGGA GAGAUUCCCU AUGGACGACA AUGGAUUAAA CCUGCAAUGU GG CGAGCAG CUAUGUGCAG UGUAGCCUGC CUUGAGUGGU GGGGGGAGAG GUUAAGUUUA AAUCUAAAGG UUAGGCCAAA CCU UUAGGC UAUUGCUUGC UGAAACCUCC AUUGCAAAAG AGGCUAGAGA UAUACCCAAC UGCCGAGGAA AUCUCCUAGA CUGU UCUAU ACGAGGUAUA UUGGGGAUUA CAGUGCGGAC UAAGUGGCAA UCCAGUCCUA UUUCUGGUGA CAGGGUAGGU AAAGC AUUA AAGGGAAACC GUCAAAAUGG CGACAUUUUG AUUGUUUUAC GGGAAAUCCU ACUGGACCUA AGCCGCAAGG UUUACU CAA UACACUACCA CCUUU

GENBANK: GENBANK: CP000726.1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 28 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260633
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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