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- EMDB-63218: Streptococcus agalactiae GOLLD RNA 3' domain decamer -

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Basic information

Entry
Database: EMDB / ID: EMD-63218
TitleStreptococcus agalactiae GOLLD RNA 3' domain decamer
Map data
Sample
  • Complex: Streptococcus agalactiae GOLLD RNA 3' domain decamer
    • RNA: RNA (700-MER)
KeywordsncRNA / RNA
Biological speciesStreptococcus agalactiae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsXie J / Peng X / Wang L / Su Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222040 China
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Streptococcus agalactiae ncRNA 3prime decamer
Authors: Xie J / Wang L / Peng X / Su Z
History
DepositionJan 18, 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_63218.png

Downloads & links

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Map

FileDownload / File: emd_63218.map.gz / Format: CCP4 / Size: 216 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.)
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: 0.0632
Minimum - Maximum-0.17412342 - 0.30384064
Average (Standard dev.)0.0017812059 (±0.011568414)
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_63218_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_63218_half_map_2.map
Projections & Slices
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Sample components

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Entire : Streptococcus agalactiae GOLLD RNA 3' domain decamer

EntireName: Streptococcus agalactiae GOLLD RNA 3' domain decamer
Components
  • Complex: Streptococcus agalactiae GOLLD RNA 3' domain decamer
    • RNA: RNA (700-MER)

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Supramolecule #1: Streptococcus agalactiae GOLLD RNA 3' domain decamer

SupramoleculeName: Streptococcus agalactiae GOLLD RNA 3' domain decamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus agalactiae (bacteria)

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Macromolecule #1: RNA (700-MER)

MacromoleculeName: RNA (700-MER) / type: rna / ID: 1 / Number of copies: 10
Source (natural)Organism: Streptococcus agalactiae (bacteria)
Molecular weightTheoretical: 226.432562 KDa
SequenceString: GCCGUCUCAA UAGUGGCUUA GCACAGAUAA UCCAUAGCGA UAUGGGAAAG CUUUUGUAGG UGUAUCAACA AGAGCGCCAG UGAUGGUCA AUCUAAGCAA ACCAAUCUUU AUGUAAUCAG UAAUGGUUAC AGCACACGAA GUCAAAGCGC AAUACCAGAG C CAAUCGGU ...String:
GCCGUCUCAA UAGUGGCUUA GCACAGAUAA UCCAUAGCGA UAUGGGAAAG CUUUUGUAGG UGUAUCAACA AGAGCGCCAG UGAUGGUCA AUCUAAGCAA ACCAAUCUUU AUGUAAUCAG UAAUGGUUAC AGCACACGAA GUCAAAGCGC AAUACCAGAG C CAAUCGGU GAGGUGCUGU GUCAGCAGUA CGUGCGACGA GUGUGUAGGA GGUAUAAACU GACGAAGUUC AAGGGUGGUA CC AAGAGCG GUCAGCAUGU UGUGCAACGC UGGGAGGAUA UCCCAGUCAA ACACAACAAG UCAAGGUGUA CCAGCACCGA GAU AACAAG UAGGCGUUGC GCAUUUUGUU GCUCAAAAGG CGACGAAACG CAAGGCAAUG CACGUCUGCG AUACACGAAA ACAA UGCUA UUUGUUGAAA AUAUUGGAAU AAAGCAAAAG UCAUUGCCCG UCGCAAACGA AAGUGUGCUU CGGUAGCUAG GCUAC CUGC UAGAGUCUCG CAAGGAUAAU AGCAAAGUCA AAGAGUAAAG CAGCUUAGAC CUUUAGCGGG GUUUUCGUUA AUUGAA AAA UGGCUUAGUA GUUUGCGGCG UAACGAGUGG UUAGCGAUAC UAACCGCGCA UGGUUGUUAC UUGAAGGGAU UUGAGUG GA UAAAAAACUA AAACAUAAGG UUUUGAAAGA CAACUGACUA AACGUGUAAU CUCAGCGU

GENBANK: GENBANK: CP007570.1

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 55.0 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: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66723
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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