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- EMDB-62191: Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor -

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Basic information

Entry
Database: EMDB / ID: EMD-62191
TitleCryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor
Map dataunsharpened map:Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor- unsharpened map
Sample
  • Complex: Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor
    • RNA: RNA (251-MER)
  • Ligand: MAGNESIUM ION
KeywordsAnabaena tRNA(Leu) precursor / Self-folding / Splicing / Cyclization / Cryo-EM / RNA
Biological speciesAnabaena (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsZhang X / Li S / Zhang K / Palo MZ / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nat Chem Biol / Year: 2026
Title: Self-splicing and cyclization mechanisms of the full-length Anabaena pre-tRNA.
Authors: Xiaojing Zhang / Linfeng An / Wen Yang / Ran Yi / Ji Liu / Shanshan Li / Kaiming Zhang /
Abstract: Group I introns are catalytic RNAs capable of self-splicing and generating circular RNAs, processes central to RNA metabolism and biotechnology. Yet, full-length ribozyme structures containing entire ...Group I introns are catalytic RNAs capable of self-splicing and generating circular RNAs, processes central to RNA metabolism and biotechnology. Yet, full-length ribozyme structures containing entire exon sequences and the structural basis of postsplicing circularization have remained limited. Using cryo-electron microscopy, we resolved multiple conformational states of the full-length Anabaena tRNA(Leu) precursor, capturing key intermediates of splicing and cyclization. In the apo state, the exons preassemble into a mature tRNA-like conformation that promotes P1 helix formation. Transitions through the splicing states involve substantial rearrangements essential for catalysis. Unlike other group I introns, the Anabaena intron circularizes without sequence loss, using its guanosine-binding site as the catalytic center. Mutational analyses confirm that G37 reorientation and a conserved wobble receptor motif precisely position the circularization site, driving efficient cyclization even in engineered PIE systems. These findings uncover unique mechanisms of RNA catalysis and establish structure-based optimization for advancing RNA circularization technologies.
History
DepositionOct 26, 2024-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62191.png

Downloads & links

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Map

FileDownload / File: emd_62191.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map:Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor- unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.024700303 - 0.18964985
Average (Standard dev.)0.00021816982 (±0.0046742237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Linear intron-1G map:Cryo-EM structure of linear intron of...

Fileemd_62191_additional_1.map
AnnotationLinear intron-1G map:Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor
Projections & Slices
AxesZYX

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Half map: Half map B: Cryo-EM structure of linear intron...

Fileemd_62191_half_map_1.map
AnnotationHalf map B: Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A: Cryo-EM structure of linear intron...

Fileemd_62191_half_map_2.map
AnnotationHalf map A: Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor

EntireName: Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor
Components
  • Complex: Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor
    • RNA: RNA (251-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor

SupramoleculeName: Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Anabaena (bacteria)
Molecular weightTheoretical: 80 KDa

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Macromolecule #1: RNA (251-MER)

MacromoleculeName: RNA (251-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Anabaena (bacteria)
Molecular weightTheoretical: 81.374578 KDa
SequenceString: GGAAAUAAUU GAGCCUUAGA GAAGAAAUUC UUUAAGUGGA UGCUCUCAAA CUCAGGGAAA CCUAAAUCUA GCUAUAGACA AGGCAAUCC UGAGCCAAGC CGAAGUAGUA AUUAGUAAGU UAACAACAGA UAACUUACAG CUAGUCGGAA GGUGCAGAGA C UCGACGGG ...String:
GGAAAUAAUU GAGCCUUAGA GAAGAAAUUC UUUAAGUGGA UGCUCUCAAA CUCAGGGAAA CCUAAAUCUA GCUAUAGACA AGGCAAUCC UGAGCCAAGC CGAAGUAGUA AUUAGUAAGU UAACAACAGA UAACUUACAG CUAGUCGGAA GGUGCAGAGA C UCGACGGG AGCUACCCUA ACGUCAAGAC GAGGGUAAAG AGAGAGUCCA AUUCUCAAAG CCAAUAGGCA GUAGCGAAAG CU GCGGGAG AAUG

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 3 / 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

Concentration1.2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1383523
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 110563
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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