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- EMDB-66618: Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron a... -

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Basic information

Entry
Database: EMDB / ID: EMD-66618
TitleCryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
Map dataCryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
Sample
  • Complex: Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
    • RNA: Azoarcus sp. BH72 self-splicing group I intron of tRNA-Ile
  • Ligand: MAGNESIUM ION
KeywordsAzoarcus sp. BH72 pre-tRNA(ILE) / second-step cyclization / c' intron / RNA
Biological speciesAzoarcus olearius (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsHong Y / Liu JS / Zhang K / Li S / Hu R / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nat Commun / Year: 2026
Title: Pre-splicing conformation and stepwise circularization of a group I intron in Azoarcus pre-tRNA
Authors: Hong Y / Liu J / Zhang X / Liu J / Li S / Zhang K
History
DepositionOct 15, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66618.png

Downloads & links

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Map

FileDownload / File: emd_66618.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.08135389 - 0.28021306
Average (Standard dev.)0.00023933059 (±0.005512679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE)...

Fileemd_66618_additional_1.map
AnnotationCryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE)...

Fileemd_66618_half_map_1.map
AnnotationCryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE)...

Fileemd_66618_half_map_2.map
AnnotationCryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
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 the Azoarcus sp. BH72 pre-tRNA(ILE) intron a...

EntireName: Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
Components
  • Complex: Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
    • RNA: Azoarcus sp. BH72 self-splicing group I intron of tRNA-Ile
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron a...

SupramoleculeName: Cryo-EM structure of the Azoarcus sp. BH72 pre-tRNA(ILE) intron after second-step cyclization (circular form)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Azoarcus olearius (bacteria)
Molecular weightTheoretical: 70 KDa

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Macromolecule #1: Azoarcus sp. BH72 self-splicing group I intron of tRNA-Ile

MacromoleculeName: Azoarcus sp. BH72 self-splicing group I intron of tRNA-Ile
type: rna / ID: 1 / Details: RNA (201-MER) / Number of copies: 1
Source (natural)Organism: Azoarcus olearius (bacteria)
Molecular weightTheoretical: 65.173973 KDa
SequenceString: CGAUGUGCCU UGCGCCGGGA AACCACGCAA GGGAUGGUGU CAAAUUCGGC GAAACCUAAG CGCCCGCCCG GGCGUAUGGC AACGCCGAG CCAAGCUUCG GCGCCUGCGC CGAUGAAGGU GUAGAGACUA GACGGCACCC ACCUAAGGCA AACGCUAUGG U GAAGGCAU ...String:
CGAUGUGCCU UGCGCCGGGA AACCACGCAA GGGAUGGUGU CAAAUUCGGC GAAACCUAAG CGCCCGCCCG GGCGUAUGGC AACGCCGAG CCAAGCUUCG GCGCCUGCGC CGAUGAAGGU GUAGAGACUA GACGGCACCC ACCUAAGGCA AACGCUAUGG U GAAGGCAU AGUCCAGGGA GUGGCGAAAG UCACACAAAC CGG

GENBANK: GENBANK: DQ103524.1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 6 / 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 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2308023
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 213341
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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