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- PDB-8xtr: Comamonas testosteroni KF-1 circularly permuted group II intron 2... -

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Basic information

Entry
Database: PDB / ID: 8xtr
TitleComamonas testosteroni KF-1 circularly permuted group II intron 2S state
Components
  • RNA (219-MER)
  • RNA (595-MER)
KeywordsRNA / CryoEM / Ribozyme
Function / homology: / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesComamonas testosteroni KF-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsWang, L. / Xie, J.H. / Zhang, C. / Zou, J. / Huang, Z. / Shang, S. / Chen, X. / Yang, Y. / Liu, J. / Dong, H. ...Wang, L. / Xie, J.H. / Zhang, C. / Zou, J. / Huang, Z. / Shang, S. / Chen, X. / Yang, Y. / Liu, J. / Dong, H. / Huang, D. / Su, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis of circularly permuted group II intron self-splicing.
Authors: Liu Wang / Jiahao Xie / Chong Zhang / Jian Zou / Zirui Huang / Sitong Shang / Xingyu Chen / Yang Yang / Jianquan Liu / Haohao Dong / Dingming Huang / Zhaoming Su /
Abstract: Circularly permuted group II introns (CP introns) consist of rearranged structural domains separated by two tethered exons, generating branched introns and circular exons via back-splicing. ...Circularly permuted group II introns (CP introns) consist of rearranged structural domains separated by two tethered exons, generating branched introns and circular exons via back-splicing. Structural and mechanistic understanding of circular RNA (circRNA) generation by CP introns remains elusive. We resolve cryo-electron microscopy structures of a natural CP intron in different states during back-splicing at a resolution of 2.5-2.9 Å. Domain 6 (D6) undergoes a conformational change of 65° after branching, to facilitate 3'-exon recognition and circularization. Previously unseen tertiary interactions compact the catalytic triad and D6 for splicing without protein, whereas a metal ion, M, is observed to stabilize the 5'-exon during splicing. While these unique features were not observed in canonical group II introns and spliceosomes, they are common in CP introns, as demonstrated by the cryo-EM structure of another CP intron discovered by comparative genomics analysis. Our results elucidate the mechanism of CP intron back-splicing dynamics, with potential applications in circRNA research and therapeutics.
History
DepositionJan 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (219-MER)
B: RNA (595-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,16038
Polymers264,1962
Non-polymers96436
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain RNA (219-MER)


Mass: 70555.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: In chain A, resid 140 - resid 210 is missed in our model.
Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Production host: synthetic construct (others) / References: GenBank: 2637094706
#2: RNA chain RNA (595-MER)


Mass: 193640.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Production host: synthetic construct (others) / References: GenBank: 2637094706
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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: Comamonas testosteroni KF-1 circularly permuted group II intron 2S state
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.251 MDa / Experimental value: NO
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: 59 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65386 / Symmetry type: POINT

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