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- EMDB-61189: lactobacillus salivarius ncRNA hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-61189
Titlelactobacillus salivarius ncRNA hexamer
Map data
Sample
  • Complex: Lactobacillus salivarius ROOL RNA hexamer
    • RNA: RNA (550-MER)
  • Ligand: MAGNESIUM ION
KeywordsCryoEM / RNA
Biological speciesLigilactobacillus salivarius DSM 20555 = ATCC 11741 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsWang L / Xie JH / Shang ST / Su ZM
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022TFC2303700 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
DepositionAug 17, 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_61189.png

Downloads & links

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Map

FileDownload / File: emd_61189.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.39228177 - 0.67908627
Average (Standard dev.)0.002083402 (±0.019462332)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61189_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_61189_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Lactobacillus salivarius ROOL RNA hexamer

EntireName: Lactobacillus salivarius ROOL RNA hexamer
Components
  • Complex: Lactobacillus salivarius ROOL RNA hexamer
    • RNA: RNA (550-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Lactobacillus salivarius ROOL RNA hexamer

SupramoleculeName: Lactobacillus salivarius ROOL RNA hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ligilactobacillus salivarius DSM 20555 = ATCC 11741 (bacteria)

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Macromolecule #1: RNA (550-MER)

MacromoleculeName: RNA (550-MER) / type: rna / ID: 1 / Number of copies: 6
Source (natural)Organism: Ligilactobacillus salivarius DSM 20555 = ATCC 11741 (bacteria)
Molecular weightTheoretical: 177.17475 KDa
SequenceString: UUAGUAUAUA AGUGUACCGA UGAAGCUAGU GGAUAAGGUG UGACAAGCCG CCUAGCCAUA CGUCUCUUAA UAACUACUAU GACGAAAUA UACGGAUACG UUUAUUUUUU CUAAUUUCCA CUUGGGUAGU ACUAAUUGGG AGCAACGAAA AAAAGUUGUG U AGAGAGAA ...String:
UUAGUAUAUA AGUGUACCGA UGAAGCUAGU GGAUAAGGUG UGACAAGCCG CCUAGCCAUA CGUCUCUUAA UAACUACUAU GACGAAAUA UACGGAUACG UUUAUUUUUU CUAAUUUCCA CUUGGGUAGU ACUAAUUGGG AGCAACGAAA AAAAGUUGUG U AGAGAGAA GCAAGGGGAC UCAUAUCUGA AACUAAGACA CUUGCCGUCA GGGAUUCGCA AUAUACCAUC UUUAGUUAAU UA AGGCUGA UUACCUUAGG AACCAACGAA GAAUAUCAAU UAAGAAUUCG UGUCGUGAAG UUGUGGUGAU GCAACUAUAA CUG ACGAGU AAGGUUUGAG UAGCCAAAAU CGACAAUCUU AUAUUAACAG AAAUAUGGAC AUUACACAUG UUUGGUGAAA AUUG GAUAG GAAAAGGUCU AUGCCCUGAA CUUGAAAUGC GGACUAGGUC AUGGAAGUUG CUAGCCAUGA UGUGCUAGUC UGAUU CAGU AGUCUAAUAA GUCCAGAUAC AAGAGUAUCC CACGUAAGCC AAUACGCGUC GGUUUACAUA AUUUUU

GENBANK: GENBANK: CP047413.1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 56 / 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 QUANTUM (4k x 4k) / Average electron dose: 63.0 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: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 270213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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