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- PDB-9lcr: Clostridium botulinum OLE RNA dimer -

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Basic information

Entry
Database: PDB / ID: 9lcr
TitleClostridium botulinum OLE RNA dimer
ComponentsRNA (578-MER)
KeywordsRNA / ncRNA / CryoEM
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesClostridium botulinum A str. ATCC 19397 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJia, X.Y. / Wang, L. / Su, Z.M.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Mar 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Mar 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2May 14, 2025Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (578-MER)
B: RNA (578-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,22630
Polymers373,5452
Non-polymers68128
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain RNA (578-MER)


Mass: 186772.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum A str. ATCC 19397 (bacteria)
Production host: synthetic construct (others) / References: GenBank: 152926829
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Clostridium botulinum OLE RNA dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Clostridium botulinum A str. ATCC 19397 (bacteria)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260633 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217382
ELECTRON MICROSCOPYf_angle_d0.58927110
ELECTRON MICROSCOPYf_dihedral_angle_d17.2928680
ELECTRON MICROSCOPYf_chiral_restr0.0293618
ELECTRON MICROSCOPYf_plane_restr0.004724

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