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- EMDB-38174: Cte-U537ins_Branch Intermediate,Ca,active -

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Basic information

Entry
Database: EMDB / ID: EMD-38174
TitleCte-U537ins_Branch Intermediate,Ca,active
Map data
Sample
  • Organelle or cellular component: Cte-U537ins_Branch Intermediate
    • RNA: RNA (219-MER)
    • RNA: RNA (590-MER)
  • Ligand: CALCIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water
KeywordsCP group ii intron / Cte / back-splicing / circular RNA / cryo-EM / SPLICING / RNA
Biological speciesComamonas testosteroni KF-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 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-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38174.png

Downloads & links

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Map

FileDownload / File: emd_38174.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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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

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0146
Minimum - Maximum-0.13413629 - 16.889135
Average (Standard dev.)-0.003297854 (±0.5848001)
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_38174_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_38174_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Cte-U537ins_Branch Intermediate

EntireName: Cte-U537ins_Branch Intermediate
Components
  • Organelle or cellular component: Cte-U537ins_Branch Intermediate
    • RNA: RNA (219-MER)
    • RNA: RNA (590-MER)
  • Ligand: CALCIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: Cte-U537ins_Branch Intermediate

SupramoleculeName: Cte-U537ins_Branch Intermediate / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)

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Macromolecule #1: RNA (219-MER)

MacromoleculeName: RNA (219-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Molecular weightTheoretical: 70.619031 KDa
SequenceString: GCCGGGGCGC CACCCCGGAA GUGAUGCGAG UCGCAACUCG CAUCACAAGC AAACGCUGUA GCCGCGUGCC UCUAAUAGGG CUGGCGCGG UUGCGAAGGG CGCUGGUGAG UGCAACUCUC ACCUUCGACC CAAUCCAUCU UGCGGCUCAA CCCCGCAAGA U CAUCGCCA ...String:
GCCGGGGCGC CACCCCGGAA GUGAUGCGAG UCGCAACUCG CAUCACAAGC AAACGCUGUA GCCGCGUGCC UCUAAUAGGG CUGGCGCGG UUGCGAAGGG CGCUGGUGAG UGCAACUCUC ACCUUCGACC CAAUCCAUCU UGCGGCUCAA CCCCGCAAGA U CAUCGCCA GACCGCUGGC GGCGUACUGA GUGACAAACG AGGCAAAACC AAAUAGAAGU U

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Macromolecule #2: RNA (590-MER)

MacromoleculeName: RNA (590-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Molecular weightTheoretical: 192.000297 KDa
SequenceString: GGGCGACCGU GAAACGGCGC UGGGCAGGAA AUGGCCCAGU GACCUGGUCA AUGGUGAAAA UCGGUGAAAG ACCGACCGGU GGGGCGUAU CGAAAGAGCG CAACGCCUGC CGCACAGGAU GGCUUCUGAG GUACCGGUGA CGGUACAGAA CGCGGAGGGG A AACCUGGA ...String:
GGGCGACCGU GAAACGGCGC UGGGCAGGAA AUGGCCCAGU GACCUGGUCA AUGGUGAAAA UCGGUGAAAG ACCGACCGGU GGGGCGUAU CGAAAGAGCG CAACGCCUGC CGCACAGGAU GGCUUCUGAG GUACCGGUGA CGGUACAGAA CGCGGAGGGG A AACCUGGA AGCGAGGGCA CCUCGGGAAA CCGGGGGUCG AUGCAUAGCU CAAACCUGUA ACGGCACCAG UGAAAGGUGC UG UGCGGAG CAACGUGGAG CCACAGGCAU GAAGCCGUGG UUCGUAGUCG AUGAGACAAG CGGUGAGUAA GGGAAGGGCU UGC GAACAU CGCCUCCCCG AAAUCCAAGG AAAGCCGAAA GGCUAGCCGC UUUGUUGAGA CAGUGGCGCC ACGUUGCGCA UUAG CCGUG ACCUAAACGG GGAACCUCUU GGCCGUACCG ACUCGGGUGG CACCGGUCGG GCUCGAUGGC UCAAGAGGGG GAGAU GUGA UGAUUAGGGU UUGACCCGUG AUGCGAUACG ACCGAAGCAU CCGGGGAGCU GUCUGACGAA GAGUCGGCAG CAGUGG GUU UGGCGACCCG CUCCGAAAGU CGCAAGC

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 15 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 6 / 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: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129492
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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