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- EMDB-62489: Fusobacterium ncRNA dimer2 -

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Basic information

Entry
Database: EMDB / ID: EMD-62489
TitleFusobacterium ncRNA dimer2
Map data
Sample
  • Complex: Fusobacterium nucleatum ARRPOF RNA dimer conformation 1
    • RNA: RNA (255-MER)
KeywordsCryoEM / RNA
Biological speciesFusobacterium nucleatum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsTu YF / Shang ST / Su ZM
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 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
DepositionNov 23, 2024-
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_62489.png

Downloads & links

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Map

FileDownload / File: emd_62489.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.44946834 - 0.9569587
Average (Standard dev.)0.001376449 (±0.015396597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62489_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62489_half_map_2.map
Projections & Slices
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Sample components

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Entire : Fusobacterium nucleatum ARRPOF RNA dimer conformation 1

EntireName: Fusobacterium nucleatum ARRPOF RNA dimer conformation 1
Components
  • Complex: Fusobacterium nucleatum ARRPOF RNA dimer conformation 1
    • RNA: RNA (255-MER)

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Supramolecule #1: Fusobacterium nucleatum ARRPOF RNA dimer conformation 1

SupramoleculeName: Fusobacterium nucleatum ARRPOF RNA dimer conformation 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: RNA (255-MER)

MacromoleculeName: RNA (255-MER) / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 82.17943 KDa
SequenceString: AAAAAACUUA CUAUUAUAUU UGUAACAAAU UUUAUACAUA AGAUAAAUUC GUAUGUAUAG CCGUUCUGCU CGAAACGGUA UAGCACCGU AAUGGUGGUA UUAUGAAUUG UAGCAAGGUG CGAGGCUACC UUUAAAAGUC UUGGAGGUGC UCUGAGUGGG U ACUUUAUU ...String:
AAAAAACUUA CUAUUAUAUU UGUAACAAAU UUUAUACAUA AGAUAAAUUC GUAUGUAUAG CCGUUCUGCU CGAAACGGUA UAGCACCGU AAUGGUGGUA UUAUGAAUUG UAGCAAGGUG CGAGGCUACC UUUAAAAGUC UUGGAGGUGC UCUGAGUGGG U ACUUUAUU AGGGUUAUAA UUUAGAAAGU AAGCUAAAAC UCUAGGUGUU GGGCAGGGCU AACACUGGCA UAUAAUUAAA UA UGCGAUA AAGUAAGU

GENBANK: GENBANK: AF295336.1

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 57.0 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: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 209916
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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