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- EMDB-38648: Comamonas testosteroni KF-1 circularly permuted group II intron 2... -

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Basic information

Entry
Database: EMDB / ID: EMD-38648
TitleComamonas testosteroni KF-1 circularly permuted group II intron 2S state
Map data
Sample
  • Complex: Comamonas testosteroni KF-1 circularly permuted group II intron 2S state
    • RNA: RNA (219-MER)
    • RNA: RNA (595-MER)
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
KeywordsCryoEM / Ribozyme / RNA
Biological speciesComamonas testosteroni KF-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsWang L / Xie JH / Zhang C / Zou J / Huang Z / Shang S / Chen X / Yang Y / Liu J / Dong H ...Wang L / Xie JH / Zhang C / Zou J / Huang Z / Shang S / Chen X / Yang Y / Liu J / Dong H / Huang D / Su Z
Funding support China, 1 items
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, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38648.png

Downloads & links

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Map

FileDownload / File: emd_38648.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0268
Minimum - Maximum-0.7807648 - 1.1609511
Average (Standard dev.)0.0007558417 (±0.01901131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38648_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38648_half_map_2.map
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Sample components

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Entire : Comamonas testosteroni KF-1 circularly permuted group II intron 2...

EntireName: Comamonas testosteroni KF-1 circularly permuted group II intron 2S state
Components
  • Complex: Comamonas testosteroni KF-1 circularly permuted group II intron 2S state
    • RNA: RNA (219-MER)
    • RNA: RNA (595-MER)
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Comamonas testosteroni KF-1 circularly permuted group II intron 2...

SupramoleculeName: Comamonas testosteroni KF-1 circularly permuted group II intron 2S state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Molecular weightTheoretical: 251 KDa

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Macromolecule #1: RNA (219-MER)

MacromoleculeName: RNA (219-MER) / type: rna / ID: 1
Details: In chain A, resid 140 - resid 210 is missed in our model.
Number of copies: 1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Molecular weightTheoretical: 70.555961 KDa
SequenceString: CCGGGGCGCC ACCCCGGAAG UGAUGCGAGU CGCCAACUCG CAUCACAAGC AAACGCUGUA GCCGCGUGCC UCUAAUAGGG CUGGCGCGG UUGCGAAGGG CGCUGGUGAG UGCAACUCUC ACCUUCGACC CAAUCCAUCU UGCGGCUCAA CCCCGCAAGA U CAUCGCCA ...String:
CCGGGGCGCC ACCCCGGAAG UGAUGCGAGU CGCCAACUCG CAUCACAAGC AAACGCUGUA GCCGCGUGCC UCUAAUAGGG CUGGCGCGG UUGCGAAGGG CGCUGGUGAG UGCAACUCUC ACCUUCGACC CAAUCCAUCU UGCGGCUCAA CCCCGCAAGA U CAUCGCCA GACCGCUGGC GGCGUACUGA GUGACAAACG AGGCAAAACC AAAUUGAAGU U

GENBANK: GENBANK: CP140157.1

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Macromolecule #2: RNA (595-MER)

MacromoleculeName: RNA (595-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Molecular weightTheoretical: 193.64025 KDa
SequenceString: GGGCGACCGU GAAACGGCGC UGGGCAGGAA AUGGCCCAGU GACCUGGUCA AUGGUGAAAG UCGGUGAAAG ACCGACCGGU GGGGCGUAU CGAAAGAGCG CAACACCUGC CGCACAGGAU GGCUUCUGAG GUACCGGUGA CGGUACAGAA CGCGGAGGGG A AACCUGGA ...String:
GGGCGACCGU GAAACGGCGC UGGGCAGGAA AUGGCCCAGU GACCUGGUCA AUGGUGAAAG UCGGUGAAAG ACCGACCGGU GGGGCGUAU CGAAAGAGCG CAACACCUGC CGCACAGGAU GGCUUCUGAG GUACCGGUGA CGGUACAGAA CGCGGAGGGG A AACCUGGA AGCGAGGGCA CCUCGGGAAA CCGGGGGUCG AUGCAUAGCU CAAACCUGUA ACGGCACCAG UGGAGGGUGC UG UGCGGAG CAACGUGGAG CCACAGGCAU GAAGCCGUGG UUCGUAGUCG AUGAGACAAG CGGUGAGUAA GGGAAGGGCU GCG AACAUC GCCUCCCCGA AAUCCAAGGA AAGCCGAAAG GCUAGCCGCU UUGUUGAGAC AGUGGCGCCA CGUUGCGCAU UAGC CGUGA CCUAAACGGG GAACCUCUUG GCCGUACCGA CUCGGGUGGC ACCGGUCGGG CUCGAUGGCU CAAGAGGGGG AGAUG UGAU GAUUAGGGUU UGACCCGUGA UGCGAUACGA CCGAAGCAUC CGGGGAGCUG UCUGACGAAG AGUCGGCAGC AGUGGG UUU GGCGACCCGC UCCGAAAGUC GCAAGCGUUU GC

GENBANK: GENBANK: CP140157.1

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 30 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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 / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 59.0 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: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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