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- PDB-8xtp: Comamonas testosteroni KF-1 circularly permuted group II intron P... -

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Basic information

Entry
Database: PDB / ID: 8xtp
TitleComamonas testosteroni KF-1 circularly permuted group II intron Post-2S state
Components
  • RNA (133-MER)
  • RNA (595-MER)
KeywordsRNA / CryoEM / Ribozyme
Function / homology: / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesComamonas testosteroni KF-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang, L. / Xie, J.H. / Zhang, C. / Zou, J. / Huang, Z.R. / Shang, S.T. / Chen, X.Y. / Yang, Y. / Liu, J. / Dong, H.H. ...Wang, L. / Xie, J.H. / Zhang, C. / Zou, J. / Huang, Z.R. / Shang, S.T. / Chen, X.Y. / Yang, Y. / Liu, J. / Dong, H.H. / Huang, D.M. / Su, Z.M.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 China
Ministry of Science and Technology (MoST, China)2021YFA1301900 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
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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
Revision 1.2Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RNA (595-MER)
A: RNA (133-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,72145
Polymers236,4962
Non-polymers1,22543
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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
#2: RNA chain RNA (133-MER)


Mass: 42855.496 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.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
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 Post-2S state
Type: COMPLEX / Entity ID: #2 / Source: RECOMBINANT
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
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: 64 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59466 / Symmetry type: POINT

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