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- EMDB-38177: Cte-U537ins-Branching,Ca,inactive -

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Basic information

Entry
Database: EMDB / ID: EMD-38177
TitleCte-U537ins-Branching,Ca,inactive
Map data
Sample
  • Organelle or cellular component: Cte-U537ins-Branching
    • RNA: RNA (811-mer)
  • Ligand: CALCIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water
KeywordsCP group ii intron / Cte / back-splicing / circular RNA / SPLICING / RNA
Biological speciesComamonas testosteroni KF-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsLing XB / Ma JB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC 31971130 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structures of a natural circularly permuted group II intron reveal mechanisms of branching and backsplicing.
Authors: Xiaobin Ling / Yuqi Yao / Jinbiao Ma /
Abstract: Circularly permuted (CP) group II introns, identified in various bacteria phyla, swap domains D5 and D6 near the 5' end and have reversed splice sites (SSs), leading to backsplicing and circular RNA ...Circularly permuted (CP) group II introns, identified in various bacteria phyla, swap domains D5 and D6 near the 5' end and have reversed splice sites (SSs), leading to backsplicing and circular RNA formation. In this study, we present multiple high-resolution cryo-electron microscopy structures of a natural CP group II intron from Comamonas testosteroni KF-1 (Cte 1), elucidating the molecular mechanisms of branching and backsplicing. During branching, the 5' SS is positioned by an auxiliary sequence (AUX)-enhanced interaction between the exon-binding site and intron-binding site (IBS) and stacks on the branch-site adenosine within D6, allowing the attacking 2'-OH group to coordinate with a metal ion in the active center. In backsplicing, the 3' SS is aligned with the branching step, leaving IBS in the active center, stabilized by base pairing with the AUX, which enables the free 3'-end hydroxyl group to directly attack the scissile phosphate of 3' SS. Furthermore, a groove in Cte 1 may stabilize the circular RNA. These findings highlight a conserved catalytic mechanism for canonical group II introns, albeit facilitated by the versatile AUX, opening avenues for designing potent ribozymes producing circular RNAs.
History
DepositionNov 30, 2023-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38177.png

Downloads & links

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Map

FileDownload / File: emd_38177.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.61
Minimum - Maximum-0.12694603 - 17.111927000000001
Average (Standard dev.)0.0010814945 (±0.60503894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38177_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38177_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cte-U537ins-Branching

EntireName: Cte-U537ins-Branching
Components
  • Organelle or cellular component: Cte-U537ins-Branching
    • RNA: RNA (811-mer)
  • Ligand: CALCIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: Cte-U537ins-Branching

SupramoleculeName: Cte-U537ins-Branching / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)

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Macromolecule #1: RNA (811-mer)

MacromoleculeName: RNA (811-mer) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Molecular weightTheoretical: 263.339688 KDa
SequenceString: GGCCGGGGCG CCACCCCGGA AGUGAUGCGA GUCGCCAACU CGCAUCACAA GCAAACGCUG UAGCCGCGUG CCUCUAAUAG GGCUGGCGC GGUUGCGAAG GGCGCUGGUG AGUGCAACUC UCACCUUCGA CCCAAUCCAU CUUGCGGCUC AACCCCGCAA G AUCAUCGC ...String:
GGCCGGGGCG CCACCCCGGA AGUGAUGCGA GUCGCCAACU CGCAUCACAA GCAAACGCUG UAGCCGCGUG CCUCUAAUAG GGCUGGCGC GGUUGCGAAG GGCGCUGGUG AGUGCAACUC UCACCUUCGA CCCAAUCCAU CUUGCGGCUC AACCCCGCAA G AUCAUCGC CAGACCGCUG GCGGCGUACU GAGUGACAAA CGGGGCAAAA CCAAAUUGAA GUUGGGCGAC CGUGAAACGG CG CUGGGCA GGAAAUGGCC CAGUGACCUG GUCAAUGGUG AAAGUCGGUG AAAGACCGAC CGGUGGGGCG UAUCGAAAGA GCG CAACAC CUGCCGCACA GGAUGGCUUC UGAGGUACCG GUGACGGUAC AGAACGCGGA GGGGAAACCU GGAAGCGAGG GCAC CUCGG GAAACCGGGG GUCGAUGCAU AGCUCAAACC UGUAACGGCA CCAGUGGAGG GUGCUGUGCG GAGCAACGUG GAGCC ACAG GCAUGAAGCC GUGGUUCGUA GUCGAUGAGA CAAGCGGUGA GUAAGGGAAG GGCUUGCGAA CAUCGCCUCC CCGAAA UCC AAGGAAAGCC GAAAGGCUAG CCGCUUUGUU GAGACAGUGG CGCCACGUUG CGCAUUAGCC GUGACCUAAA CGGGGAA CC UCUUGGCCGU ACCGACUCGG GUGGCACCGG UCGGGCUCGA UGGCUCAAGA GGGGGAGAUG UGAUGAUUAG GGUUUGAC C CGUGAUGCGA UACGACCGAA GCAUCCGGGG AGCUGUCUGA CGAAGAGUCG GCAGCAGUGG GUUUGGCGAC CCGCUCCGA AAGUCGCAAG C

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 19 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126130
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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