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- EMDB-61125: Enterococcus faecalis ncRNA octamer -

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Basic information

Entry
Database: EMDB / ID: EMD-61125
TitleEnterococcus faecalis ncRNA octamer
Map data
Sample
  • Complex: Enterococcus faecalis ROOL RNA octamer
    • RNA: RNA (580-MER)
KeywordsCryoEM / RNA
Biological speciesEnterococcus faecalis JH1 (bacteria) / Enterococcus faecalis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang L / Xie JH / 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
DepositionAug 8, 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_61125.png

Downloads & links

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Map

FileDownload / File: emd_61125.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 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-0.12698351 - 0.37408087
Average (Standard dev.)0.0020694172 (±0.013734289)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61125_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_61125_half_map_2.map
Projections & Slices
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Sample components

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Entire : Enterococcus faecalis ROOL RNA octamer

EntireName: Enterococcus faecalis ROOL RNA octamer
Components
  • Complex: Enterococcus faecalis ROOL RNA octamer
    • RNA: RNA (580-MER)

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Supramolecule #1: Enterococcus faecalis ROOL RNA octamer

SupramoleculeName: Enterococcus faecalis ROOL RNA octamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Enterococcus faecalis JH1 (bacteria)
Molecular weightTheoretical: 1.45 MDa

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Macromolecule #1: RNA (580-MER)

MacromoleculeName: RNA (580-MER) / type: rna / ID: 1 / Number of copies: 8
Source (natural)Organism: Enterococcus faecalis (bacteria)
Molecular weightTheoretical: 187.837453 KDa
SequenceString: AAUUGAAAAA UCAAUAGAUU UAAACCUAGU GAAGAGCAUU UGAACAAUGU GCUAGGGUAG UAUGGGAUAA GUCGAUAACU AAAAUGAAU UGGGAUACUG AUUGAUUUUA GUGGUGGAUU UUACAGCAAU GUAAAAAGGA CUAAUAGUAA AAGCUAUUAA U CGCAAAGU ...String:
AAUUGAAAAA UCAAUAGAUU UAAACCUAGU GAAGAGCAUU UGAACAAUGU GCUAGGGUAG UAUGGGAUAA GUCGAUAACU AAAAUGAAU UGGGAUACUG AUUGAUUUUA GUGGUGGAUU UUACAGCAAU GUAAAAAGGA CUAAUAGUAA AAGCUAUUAA U CGCAAAGU ACUACGUGGA AUUUGUGCAG GUGUAAGGUA CGAAACUUUC GAGUGUGACA AUAGACGCUC CAGUGGAGAA UA AUCUAAG UUAGGUGGAA GUGUGAGAAG CUUGGCAGAC CUUAGAAAAC UCAAACCAAG CGCUUUGCAG AGAAACUGAG AAA UCAGUG UUUAACGAAA GAAGUCGGUA CGAGUAGCUU AAUGCAGCAA UUUAUUUACA GAUGACAAAU AAUAAAAAUG GGAC UCUUA UGUAAAUGCU GAAUGUUCAA GUGAAAGUUA UUAGCCAGUA GAGCUAGAUC AUACAGAAAA AGCAAAGAGA AGCUA UUGG GUAGCGCCCG AUAGUUCAGC CUCUUUGGGU AUGUGACUGA AUAACACUGU AAACAAAGGA AGCAGGAAGA AAAGCC UAA AUCUGUUGAU UUUUGAG

GENBANK: GENBANK: CP060804.1

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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: 7.9
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: 61.0 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76703
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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