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- EMDB-38649: Comamonas testosteroni KF-1 circularly permuted group II intron P... -

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Basic information

Entry
Database: EMDB / ID: EMD-38649
TitleComamonas testosteroni KF-1 circularly permuted group II intron Pre-1S state
Map data
Sample
  • Complex: Comamonas testosteroni KF-1 circularly permuted group II intron Pre-1S state
    • RNA: RNA (814-MER)
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
KeywordsCryoEM / Ribozyme / RNA
Biological speciesComamonas testosteroni KF-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsWang L / Xie JH / Zhang C / Zou J / Huang ZR / Shang ST / Chen XY / Yang Y / Liu J / Dong HH ...Wang L / Xie JH / Zhang C / Zou J / Huang ZR / Shang ST / Chen XY / Yang Y / Liu J / Dong HH / Huang DM / Su ZM
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 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_38649.png

Downloads & links

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Map

FileDownload / File: emd_38649.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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: 0.025
Minimum - Maximum-1.0423957 - 1.4281366
Average (Standard dev.)0.00084453693 (±0.020759761)
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_38649_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38649_half_map_2.map
Projections & Slices
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Sample components

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

EntireName: Comamonas testosteroni KF-1 circularly permuted group II intron Pre-1S state
Components
  • Complex: Comamonas testosteroni KF-1 circularly permuted group II intron Pre-1S state
    • RNA: RNA (814-MER)
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION

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

SupramoleculeName: Comamonas testosteroni KF-1 circularly permuted group II intron Pre-1S state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Molecular weightTheoretical: 255 KDa

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Macromolecule #1: RNA (814-MER)

MacromoleculeName: RNA (814-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Molecular weightTheoretical: 264.241188 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 UGGGCGACCG UGAAACGGCG CU GGGCAGG AAAUGGCCCA GUGACCUGGU CAAUGGUGAA AGUCGGUGAA AGACCGACCG GUGGGGCGUA UCGAAAGAGC GCA ACACCU GCCGCACAGG AUGGCUUCUG AGGUACCGGU GACGGUACAG AACGCGGAGG GGAAACCUGG AAGCGAGGGC ACCU CGGGA AACCGGGGGU CGAUGCAUAG CUCAAACCUG UAACGGCACC AGUGGAGGGU GCUGUGCGGA GCAACGUGGA GCCAC AGGC AUGAAGCCGU GGUUCGUAGU CGAUGAGACA AGCGGUGAGU AAGGGAAGGG CUGCGAACAU CGCCUCCCCG AAAUCC AAG GAAAGCCGAA AGGCUAGCCG CUUUGUUGAG ACAGUGGCGC CACGUUGCGC AUUAGCCGUG ACCUAAACGG GGAACCU CU UGGCCGUACC GACUCGGGUG GCACCGGUCG GGCUCGAUGG CUCAAGAGGG GGAGAUGUGA UGAUUAGGGU UUGACCCG U GAUGCGAUAC GACCGAAGCA UCCGGGGAGC UGUCUGACGA AGAGUCGGCA GCAGUGGGUU UGGCGACCCG CUCCGAAAG UCGCAAGCGU UUGC

GENBANK: GENBANK: CP140157.1

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 38 / 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

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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: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 302316
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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