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- EMDB-65891: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state -

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Basic information

Entry
Database: EMDB / ID: EMD-65891
TitleCryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state
Map dataunsharpened map: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state - unsharpened map
Sample
  • Complex: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state
    • RNA: RNA(334-MER)
KeywordsAnabaena tRNA(Leu) precursor / Self-folding / Splicing / Cyclization / Cryo-EM / RNA
Biological speciesAnabaena (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.28 Å
AuthorsZhang X / Li S / Zhang K
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
DepositionAug 19, 2025-
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_65891.png

Downloads & links

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Map

FileDownload / File: emd_65891.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state - 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: 0.03
Minimum - Maximum-0.0138696 - 0.111850664
Average (Standard dev.)0.0003201523 (±0.004290633)
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: sharpened map: Cryo-EM structure of Anabaena tRNA(Leu) precursor...

Fileemd_65891_additional_1.map
Annotationsharpened map: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state - sharpened map
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 Anabaena tRNA(Leu)...

Fileemd_65891_half_map_1.map
AnnotationHalf map A: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B: Cryo-EM structure of Anabaena tRNA(Leu)...

Fileemd_65891_half_map_2.map
AnnotationHalf map B: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state
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 Anabaena tRNA(Leu) precursor at Pre-2S state

EntireName: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state
Components
  • Complex: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state
    • RNA: RNA(334-MER)

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Supramolecule #1: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state

SupramoleculeName: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Anabaena (bacteria)
Molecular weightTheoretical: 108 KDa

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Macromolecule #1: RNA(334-MER)

MacromoleculeName: RNA(334-MER) / type: rna / ID: 1
Source (natural)Organism: Anabaena (bacteria)
SequenceString: GGGGGUGUGG CGGAAUGGUA GACGCUACGG ACUUAAAUAA UUGAGCCUUA GAGAAGAAAU UCUUUAAGUG GAUGCUCUCA AACUCAGGGA AACCUAAAUC UAGCUAUAGA CAAGGCAAUC CUGAGCCAAG CCGAAGUAGU AAUUAGUAAG UUAACAACAG AUAACUUACA ...String:
GGGGGUGUGG CGGAAUGGUA GACGCUACGG ACUUAAAUAA UUGAGCCUUA GAGAAGAAAU UCUUUAAGUG GAUGCUCUCA AACUCAGGGA AACCUAAAUC UAGCUAUAGA CAAGGCAAUC CUGAGCCAAG CCGAAGUAGU AAUUAGUAAG UUAACAACAG AUAACUUACA GCUAGUCGGA AGGUGCAGAG ACUCGACGGG AGCUACCCUA ACGUCAAGAC GAGGGUAAAG AGAGAGUCCA AUUCUCAAAG CCAAUAGGCA GUAGCGAAAG CUGCGGGAGA AUGAAAAUCC GUUGACCUUA AACGGUCGUG UGGGUUCAAG UCCCUCCACC CCCA

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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

Concentration2 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 3749326
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 37706
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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